Alzheimer’s Disease (AD) is one of the leading causes of death in the United States. Studies suggest that the root cause of AD is due to two proteins, Aβ1-42 and tau, which accumulate and aggregate into amyloid plaques and neurofibrillary tangles, respectively. Current studies on the heritability and genetic foundation for AD are not well resolved. In order to understand which genes are best able to resist the effects of Aβ1-42 and tau, we utilized an AD fruit fly model. More specifically, we used a mutant line of Drosophila melanogaster, which we call R32, in which human transgenes of Aβ1-42 and tau are expressed in the fly eye. We used this reagent to express AD proteins in the Drosophila Genome Reference Panel (DGRP), a set of 200 fully sequenced, inbred lines derived from a wild population, in order to simulate a model of natural genetic variation. Aβ1-42 and tau proteins lead to degradation in the eyes causing fusions and irregular shaping of ommatidia. Accordingly, we imaged fly eyes at 28 days of age. We found significant genetic variation in ommatidial circularity and area, two measures of eye quality. We performed a genome-wide association study to identify specific single nucleotide polymorphisms (SNPs) that act as markers signaling degradation in the ommatidia. Significant SNPs were found linked to genes associated with neurotransmitter receptors, neural signalling, and photoreceptor differentiation. Further studies will try to validate the effect of the identified genes and quantify the effects of the SNPs on the degenerative eye phenotype. Additionally, metabolomic studies as well as a model that expresses the AD-related proteins in the brain would be utilized to study the effects on lifespan, memory, and locomotion.

This study explores the sustainability performance of international companies in the food and beverage industry. The research goal is to investigate whether sustainability performance is correlated (positively or negatively) or is not correlated with financial performance. The Global Reporting Initiative’s sustainability reporting framework, called GRI, provides principles and metrics for reporting corporate environmental and social responsibility impacts. The Financial Accounting Standards Board financial reporting framework, called generally accepted accounting principles (GAAP), is used to prepare corporate financial reports. Both the GRI and GAAP frameworks provide consistency, so report users can analyze a company’s performance over time as well as in comparison to competitors. The Sustainability Performance Assessment (SPA) System developed by Paun (2015) incorporates GRI and GAAP measures for reporting triple bottom line performance (i.e., financial, environmental, human rights, labor practices, product responsibility, society, economic). Using the SPA System, data was extracted from 2016 sustainability and financial reports and analyzed in terms of the following multi-dimensional performance variables: environmental, human rights, labor practices, product responsibility, society, economic, revenue, leverage, and profit. The sample companies are based in Europe and the U.S. Their 2016 revenues ranged from $8.9 billion to $91.5 billion and employees ranged from 42,000 to 328,000. Data was analyzed using descriptive statistics (e.g., performance mean, degree of transparency, transparency weighted performance mean). Preliminary research findings suggest that correlations exist among the triple bottom line sustainability variables. This research reveals broader trends about the impacts of multi-national companies on the consumers they support and environment they influence.

Reports have shown the importance of student engagement and student-centered pedagogies in biology classes. A sense of community in a classroom can help students be less isolated from their peers and increase their willingness to answer questions, as well as their willingness to ask for help. This classroom sense of community can enhance students’ perception of learning and can be achieved online. Furthermore, a sense of community among underrepresented groups (URG), which have the highest attrition rates in STEM, can be a powerful tool for increasing student retention.  We hypothesize that blogging enhances a sense of community and connectivity among students. Our study analyzed 82 students’ interactions during a semester-long writing assignment in a biology class for non-biology majors at Emory University. Half of the students submitted their assignments as blog posts, the other half through a traditional educational content management system. Both groups had equivalent distributions of diverse ethnicities. Student connectivity was incentivized and monitored by having students turn in editor-sheets, reporting whose assignment they edited, and how. This student connectivity was subsequently analyzed via a Network Analysis.  Student surveys showed trends of higher perceived sense of community among bloggers relative to traditional writers. The network analysis revealed double the average connectivity among bloggers, with 2-folds higher average connections per student in the blogging group. Students also showed more evenly distributed connections among bloggers relative to traditional writers.  We conclude that the use of blogging among non-biology majors can facilitate student-student interactions and has the potential to create a sense of community, which has positive implications in the retention of under-represented groups in STEM fields.

The President’s Council of Advisors on Science and Technology estimates that the United States will need to increase its number of science, technology, engineering, and mathematics (STEM) professionals by 34% over the next decade. This guidance seems contrary to the rising trend of STEM majors becoming increasingly selective of the students they admit. Competitive degrees with additional requirements for entry (ARE) are a universally accepted phenomenon here at UW. However, there are no studies characterizing their prevalence in higher education or investigating their impact on students. We are conducting an exploratory study to characterize the number of STEM degrees across the U.S. with ARE and the factors departments use to admit students. First, we compiled institutional data for the research universities (R1) and Master’s-granting institutions with the highest number of undergraduates in each state. Next, we determined whether or not they offered STEM degrees with ARE. Programs were identified through a combination of data-mining institutional websites and contacting individuals at each institution. Finally, we administered an online survey to each department to gain deeper insight into the factors used in their admission decisions. We hypothesized that variables such as high school GPA, university GPA, and SAT score will commonly be used in the decisions to admit students. SAT scores and GPA often have significant socioeconomic and demographic biases. Consequently, if we confirm our hypothesis, this could raise questions about the equity of the admission processes for selective degrees. Preliminary results revealed over 250 degrees with ARE. Most of those degrees are offered in biology, health science, or engineering departments at R1 institutions. Ultimately, our results will inform a future study that will take a closer look at the impacts of degrees with ARE on STEM retention and diversity from a representative sample of institutions.

As the field of genomics continues to grow, there is an overwhelming need for robust ways to assemble entire genomes, yet there is little guidance on what software best achieves this goal. An assessment of available genome assemblers is needed to improve assembly procedures. Genome assemblers output draft assemblies consisting of DNA scaffolds that are permeated with errors inherent to sequencing data, like wrong number of repeats, misjoins, inversions, missing sequencing, and extraneous sequences. These draft assemblies can then be input into an experimental assay called HiC that attempts to fix and orient the assemblies by taking into account chromatin contact interactions to elucidate genome architecture. The resulting genome is then more accurate and useful for research purposes. However, given the plethora of genome assembly and HiC software available, navigating each available software is time consuming and often requires extensive testing before actual use can begin. To improve this process, we aim to review several HiC scaffolding software tools for performance and quality, and fine tune their parameters for optimized outcome. This will allow us to suggest which software work best for a range of genomic data as well as provide summary statistics and accuracy measurements for each genome assembler tested. We tested several genome assemblers, including GRAAL and SALSA, which utilize HiC libraries to scaffold draft assemblies. After being produced and corrected through assemblers, these assembled genomes can then be used to advance research in functional genomics, genetic epidemiology, and many other fields reliant on genomic data. It is our goal to improve genome assembly procedures so that more researchers can use open source software to build and understand entire genomes and further the field of genomics.

Alzheimer’s Disease (AD) is a progressive brain disorder that results in middle to late life dementia. AD, the most common form of dementia, is the sixth leading cause of death in the United States, and the third leading cause of death for older people over 65 years of age. AD is pathologically characterized by the accumulation and aggregation of an alternatively spliced amyloid-beta (Aβ) and hyperphosphorylated tau, which lead to the formation of neuritic plaques and neurofibrillary tangles (NFT’s) in the brain and ultimately to decreased neural function and cell death. Previous studies indicate that the extent to which an individual is affected by the interaction of these proteins and the severity of AD is largely influenced by genetic variation. However, the specific genes involved, their regulation and expression remain largely unknown. Our ongoing project explores the genetic variation underlying Drosophila susceptibility to severe eye cell degeneration caused by human Aβ and tau. We express Aβ and tau in the fly eye through the UAS-GAL4 system to create our AD model Drosophila, and cross them with a panel of flies (the Drosophila Genome Reference Panel, DGRP) that allows us to map natural genetic variation for resistance to Aβ and tau. Our preliminary results show significant variation in neuronal eye cell degeneration among DGRP lines, implying that neurodegeneration would also differ between DGRP lines if Aβ and tau were expressed in the nervous system. Based on current progress, this new project will continue exploring variation in DGRP lines, but this time we will express them in the fly brain. I will measure how different genotypes shape the effect of brain-specific Aβ and tau on lifespan and protein aggregation, and will use Genome Wide Association Studies to identify single nucleotide polymorphisms associated with variation in expression of Aβ and tau.

According to a January 2017 Point-in-Time count, there were over 11,000 individuals experiencing homelessness in the Seattle/King County region, with approximately 30% of those individuals under the age of 25. The University District of Seattle has been designated as an area needing special attention and increased funding to support homeless youth and young adults. Our proposal is to create an urban community café (The Doorway Café) to bridge the strengths of the University District with the social, legal, and health care needs of local homeless and food insecure youth in one centralized location. We predict that the creation of a navigation center/café will allow for an improved system of integrated services, ultimately leading to housing security and improved health outcomes. We conducted a qualitative study consisting of twenty in-depth, semi-structured interviews with homeless youth in the University District. Interviews were recorded, transcribed, and thematically analyzed to highlight data pertaining to personal lived experiences of homelessness, basic needs, and services to integrate into The Doorway Café. Preliminary thematic analysis suggests that having stable housing is a necessary prerequisite for youth and young adults to care for their other basic needs, such as health care. Interviewees expressed that the most successful café would feel safe and the resources offered would be low-barrier. The results of our research inform the services The Doorway Café should offer based on the responses of local homeless youth. Future research should explore the role that The Doorway Café has in continuity of services and in increasing housing stability among youth in the University District.

As more technology that utilizes personal electronic devices (PEDs) are being integrated in classrooms, the possibility of cell phone distraction is a real concern amongst many educators. Because of this, we became interested in cell phone use patterns in highly interactive biology classrooms at UW, and what factors influence their use. To answer this, we investigated the impact of in-class polling using PEDs or using clickers (older, standalone devices). We compared cell phone use in two different quarters (same course, same instructor) that either used PEDs or clickers for in-class polling. We also compared the cell phone use in the beginning of quarter vs. the end. In addition, we looked at whether classroom seat location correlates with cell phone use. To assess cell phone use, we directly observed active learning introductory biology lectures. Three to four researchers observed each seat in a designated section of the lecture hall and noted if a cell phone was visible (used as a proxy for use), three to five times during a class session. We used logistic regression and model selection to find a best fit model to determine if polling technology type, seat location or time of quarter (beg. vs end.) can predict cell phone visibility. To our surprise, the results indicated that neither Poll Everywhere nor time of quarter increased the already low cell phone visibility. However, our results also indicated that students that are sitting away from professor (back of classrooms) are more likely to use their cell phone than their peers regardless of polling technology. Taken together, we suggest instructors with highly interactive classrooms should not worry about integrating newer polling technologies. Further, instructors may look into having more TAs or peer facilitators roam around the classroom, especially in the case of large lecture halls to avoid cell phone misuse.

International Transracial Adoption (ITRA) is something that became popular in the 1950’s and adoptions from Asia has accounted for approximately half. International adoption occurs when a child from one country is adopted into another. Transracial adoption is the phenomena of adoption across racial and ethnic identities. While popular, the effects of ITRA on racial and adoptee identity formation are still unknown. The study focuses on the Adoptee Mentorship Program (AMP) and AMP’Lified Program that teach International Transracial Adoptees (ITRAs) from Asia about racial and adoptee identity while building community. This study aims to understand how a mentorship program could affect the adoptee and racial identity formation process for other adoptees ages 5-18. The study used a series of program evaluation surveys to determine the effects of the mentorship program on adoptee and racial identity formation. It is hypothesized that the mentorship program will allow ITRAs to develop a stronger sense of their racial and adoptee identity. This was measured through several short answer and likert scale questions focusing on how the adoptee identifies themself as an Asian and as an adoptee. Questions measured self-esteem, knowledge around race and adoption, and whether or not the ITRAs felt a sense of community from the mentorship program. The pre and mid-way survey were conducted in November and March respectively. It is believed that data from these two surveys will show a positive correlation between the AMP and AMP’Lified Programs and the racial and adoptee identity formation for the youth. The final survey will be conducted at the end of the program in June and researchers hypothesize the program will continue to strengthen the racial and adoptee identity of ITRAs. Understanding the effects of mentorship programs on adoptee and racial identity formation for ITRAs will allow for better post-adoption resources and services for adoptees.

Chronic low back pain (CLBP) poses a major public health burden, affecting 31% of the general population and 54% of older adults. Among individuals with CLBP, multisite pain increases the risk for persistent pain and can lead to physical and mental impairments. Despite this, multisite pain research is limited and little is known about its relationship with health-related quality of life (HRQoL). This study describes the effect of multisite pain on HRQoL and the association between multisite pain and falls in older adults with CLBP. We conducted a secondary analysis using the Back Pain Outcomes using Longitudinal Data (BOLD) registry. BOLD consists of 5,239 participants, ≥65 years, from three health systems, with new primary care visits for back pain. We identified 899 participants with CLBP (>2/10 pain intensity, 6 months after new visit) and assessed comorbid pain at 6 pain sites, including widespread pain. Outcomes of HRQoL (EQ-5D, scored 0-1) and falls prevalence in the past 3 weeks were evaluated 6 and 18 months after participants met the chronic pain criteria. We used linear and logistic regression models to test the relationship between number and type of pain sites with outcomes, adjusting for demographics and health characteristics. Widespread pain (b=-0.035; CI: -0.058, -0.012) and pelvic/groin pain (b=-0.027; CI: -0.050, -0.004) sites were associated with lower HRQoL. For each additional pain site, HRQoL scores decreased an average of 0.013 points (95% CI: -0.020, -0.007) and odds of a fall increased 30% (OR, 1.30; CI: 1.12, 1.51) with nearly all falls occurring in those with >1 pain site (>95%). Number of pain sites had stronger associations with decreasing HRQoL than individual pain sites. Multisite pain increased the risk for falls. Clinicians and researchers should assess multisite pain as a potential risk factor for low HRQoL and falls in older adults with CLBP.

Since 1989, over 2,000 individuals have been exonerated of crimes for which they were convicted. Of the 350+ of these individuals that were demonstrated to be innocent following post-conviction DNA testing, eyewitness misidentification was the single greatest contributor to their wrongful convictions. Given this emerging knowledge, policies have recently been adopted that recommend all identification procedures be video-audio recorded and conducted by an administrator that does not know which individual in the array is the suspect (i.e., blind). If one is not available, a “blinded” procedure is recommended in which the individual photographs are shuffled so that the administrator is unaware of where the suspect is located in the array. These recommendations developed out of the belief that they may produce more reliable evidence and increase observers’ abilities to discriminate between accurate and inaccurate witnesses. To date, studies examining third-party observers’ evaluations of videotaped identification procedures have exclusively relied on student samples. The current research extends our knowledge of third-party observers’ evaluations of recorded identification procedures through recruitment of community members (n=281) and prosecutors/defense attorneys(n=51). Participants viewed a recorded identification procedure in which the witness identified either a guilty or innocent suspect and were later asked to make judgments on the accuracy of the identification and perceptions of the witness and administrator. These procedures varied in presentation format (simultaneous/sequential) and administration type (blind/blinded/non-blind). Preliminary results show that defense attorneys displayed a disbelief bias in which they were more skeptical of identifications compared to prosecutors and community members. Secondly, observer’s perceptions of the ease of the witness’s decision and witness confidence predicted observer belief. Lastly, the ability to discriminate between accurate and inaccurate identifications was the lowest in the blinded administrations. These findings indicate a need for further research in the use of alternative administrations when a blind administration is not possible.

The ability to regulate emotion does not develop completely until young adulthood, meaning teenagers are at risk for disorders associated with difficulties in regulating emotions. Identifying one’s emotions is essential for taking active steps towards regulating them; thus emotion differentiation is an essential skill that facilitates psychological well being. Although there have been multiple questionnaires developed to assess emotion differentiation, there are limitations of self-report. Behavioral tasks provide an opportunity to observe an individual’s ability to identify emotions. The Photo Emotion Differentiation (PED) task is a computer task designed to assess emotional differentiation, validated predominantly in adult populations. Participants are shown 20 standardized emotional images and are asked to report the intensity with which they experience each of the 19 listed emotions. The limitation to this method is that it has only been used once in child populations. We aim to validate the PED for use in adolescents by comparing it to a self-report questionnaire [the Levels of Emotional Awareness Scale for Children (LEAS-C)] that assesses emotion differentiation. The instructions for the LEAS-C ask youth to respond to 12 scenarios by indicating how they might feel and how the other person in the scenario might feel. A validated scoring system is used applying specific criteria to the emotion words used in the response. This is an ongoing study and we have currently recruited 14 participants from ages 13 to 16 who will come for a lab visit and complete both the PED and the LEAS-C. A positive correlation between the scores from the PED and LEAS-C will show that the PED is measuring the construct of emotion differentiation and can be used to obtain valid assessment in youth in subsequent studies. With this information, the PED can be used to examine the relationship between pain and emotion differentiation in adolescents.

The south Puget Sound region has a history of smelting activity, notably the ASARCO smelter that operated in Ruston, WA. Despite the smelter being closed, the consequences of this smelting activity are still felt today. Due to high levels of arsenic contamination in the region’s soils, the area was designated a SuperFund site. Preliminary research conducted in 2014 indicated that several urban lakes in the Tacoma/Federal Way area also have high levels of arsenic in their sediments. If the arsenic is mobilized into the water column, where it can be taken up by lake biota and biomagnify up the food chain, it could potentially affect human health and ecosystem health. We examined two lakes, Angle Lake and Lake Killarney, that have the same amount of arsenic in their sediments, but different physical properties likely impact the release of arsenic into the water column. Angle is seasonally stratified, while Killarney remains well-mixed all year. Consequently, the bottom waters of Angle Lake stay at a relatively stable temperature of 4-10°C and consistently have arsenic concentrations between 30-100 ppb year-round. In contrast, bottom waters in Lake Killarney warm significantly from 4°C in the winter to 21°C in the summer and arsenic concentrations increase from 75 ppb to 700-1000 ppb. We hypothesize that temperature is the primary control on the release of arsenic from the sediments. To test this hypothesis, sediment cores were taken from each lake and placed into plastic tubes. To test this hypothesis, sediment cores were collected from each lake in the winter when all lakes have low bottom water temperatures. The cores were placed into two different temperature treatments, 10°C and 20°C. Samples of the water overlying the cores will be taken every week and measured using ICP-MS to determine the flux of arsenic out of the sediments.

Heterotopia are organized structures consisting of mixed elements of neurons, glia and neuronal progenitors arranged in an architectural pattern inappropriate to the considered tissue. Heterotopia are observed in pathological preparations of the cerebral cortex and the cerebellum as a feature of many neurological disorders yet the mechanisms driving their development remain unclear. We have analyzed 28 Dandy Walker Malformation (DWM) human fetal cerebella and found that more than 40% of cases contain heterotopia. DWM is the most common structural birth defect of the human cerebellum and is characterized by hypoplasia and foliation defects. A subset of cases are caused by loss of FOXC1, a transcription factor expressed in the mesenchyme adjacent to the developing cerebellum. We previously reported that in mice, loss of FOXC1 causes loss of the mesenchyme-secreted factor SDF1-alpha. Further, loss of SDF1-alpha is sufficient to cause cerebellar heterotopia, highlighting the importance of mesenchymal signaling in the maintenance of the highly stereotypical laminar architecture of the mature cerebellum. We hypothesized that granule neuronal progenitors (GCPs) adjacent to the mesenchyme are the primary cellular target of SDF1-alpha mesenchymal signaling and thus, the primary cell type driving heterotopia formation. To test our hypothesis, we specifically deleted the SDF1-alpha receptor from just GCPs using a Cre-loxP genetic scheme in mice. We determined that loss of SDF1-alpha in just this one cell type caused their premature migration into the developing cerebellar anlage and secondarily caused other cerebellar cell types to form structured heterotopia. We also observed defects in cerebellar foliation in the treatment group. Our data further highlights the importance of SDF1-alpha dependent mesenchymal signaling in cerebellar development and identifies heterotopia as a new phenotype in DWM.

Heat exposure is associated with several potential adverse heat health effects, including heat-related illness and kidney injury, for example in outdoor workers who labor in the heat. In order to best study and prevent these heat effects, accurate assessment of personal ambient heat exposure is needed. An iButton® is a small coin-shaped data-logging thermometer that can measure and log ambient temperature and humidity. The iButton® has been adapted for use in environmental human health research as an easy to use and affordable data logger for personal ambient temperature measurements. The degree to which personal iButton® measurements are influenced by heat generated by the human body, for example during physical exertion, or solar radiation (iButtons® are contained in stainless steel cases), has not been systematically described. The goal of this study is to quantify the radiated body heat from subjects exercising in both direct sunlight and shaded settings. We recruited a sample of 15 adults, who participated in sessions that were roughly two hours long, with half of the time in a shaded area followed by the same activities in direct sun. Ambient temperature was recorded using iButtons® attached to participants as well as two, five, and ten feet away. Data collected will be analyzed using R 3.4.2 data analysis software. Preliminary results suggest that monitors attached to the participant capture the release of some body heat but that this dissipates by two feet away from the participant. Preliminary results also suggest that, while monitors positioned facing the sun capture some of the effects of solar radiation, monitors in the shade or facing away from the sun do not. This information is expected to contribute to the interpretation of personal ambient temperature measurements used in future studies that examine the relationship between heat exposure and health effects.

Speech-language pathologists (SLPs) evaluate voice quality using perceptual judgments, an important method for assessing voice disorders. Ideally, perceptual judgments exhibit both intrarater reliability, in which one listener rates voices consistently, and interrater reliability, in which different listeners rate the same voices similarly. In practice, several sources of perceptual variability confound reliability, including the scaling method itself. SLPs typically use visual analog scales (VAS), in which a response is recorded along a continuous scale between two endpoints (e.g., normal to severely breathy). While other scaling methods may be more reliable than VAS, they present challenges for practical application. Visual sort and rate (VSR) is a promising scaling method, in which a listener rates voice samples using a VAS, and each voice sample serves as a perceptual reference point for other samples in the set. My study will determine 1) whether VSR yields greater intrarater and/or interrater reliability than traditional VAS in ratings of speakers with voice disorders by inexperienced listeners, and 2) whether this effect occurs for both overall severity (OS) and an isolated perceptual dimension (breathiness). I recruited five SLPs (“expert listeners”) and 20 inexperienced listeners. I sorted fifty voice samples into six sets, with a variety of severity levels in each set based on ratings by the expert listeners. To measure intrarater reliability, I repeated 20% of the samples. I instructed the inexperienced listeners to rate the samples for OS and breathiness, using both VAS and VSR. I varied task order (VAS/VSR) and dimension order (OS/breathiness) to control for learning effects. I will analyze the inexperienced listeners’ ratings to determine whether VAS or VSR yields greater intrarater and interrater reliability. I hypothesize that VSR will produce more reliable ratings of OS and breathiness. Results of my study may support clinical application of VSR for voice assessment.

Chronic pancreatitis (CP) is a condition in which the pancreas is consistently inflamed, resulting in pain, malabsorption of nutrients, and irreversible organ damage. CP-related pain can be severe and is associated with decreased quality of life and impaired psychosocial functioning. Treatment options for CP, particularly for pain management, are extremely limited in both scope and efficacy. It is imperative that additional pain therapies be made available to the CP population. Cognitive behavioral therapy (CBT) is a non-pharmacological treatment that has shown benefits in helping people cope with painful conditions. This study aimed to 1) adapt an established online CBT program (The Pain Course) for people with CP pain, 2) assess feasibility and acceptability of the program, and 3) conduct a pilot randomized controlled trial to determine preliminary efficacy of the program. We first adapted The Pain Course through careful review of the existing five lessons and case stories to insert information about CP and its symptoms to increase the relevancy of the program for CP patients. In the second phase of the project, 10 CP patients will receive access to the modified online course (The Pancreatitis Pain Course) and will complete the intervention to learn cognitive-behavioral pain coping skills. Patients will provide qualitative feedback regarding their experience and the acceptability of the intervention through interviews, and the course will be modified further. In the final phase, 30 patients will be randomized (15 patients will receive CBT and 15 will receive waitlist control condition). Outcome data on pain, psychological functioning, and quality of life will be obtained at baseline, 8 weeks, and at three-month follow up to assess treatment efficacy. Ultimately the goal is to develop a safe, economical treatment option for those who suffer from CP pain that will alter and expand current clinical practice of CP pain management.  

Traumatic brain injury (TBI) afflicts people of all ages, with older adults having the highest rates of TBI-related hospitalizations and deaths among all age groups. Many of the issues and complications that TBI patients face are mediated by the immune response. Aging is a complex process which results in a decline of the immune system due to the altering of cellular production, proliferation and function resulting in an overall decline of immunocompetence. Injury sets off a chain reaction of immune cellular responses, the cell of interest in this project is TH2 cells, which have been shown to play a role in chronic inflammation. The purpose of this study was to explore if the age of an individual influences the TH2 cellular response in relation to traumatic brain injury. The TH2 cells used in the study were collected from younger (aged 21-64) and older (aged 65+) adult participants at < 24hours following mild/moderate TBI and at 3 months post injury. TH2 cells were stimulated with phytohaemagglutinin (PHA) and anti-CD3 and then incubated overnight. They were then analyzed for IL-5 production using the ELISpot assay. The number of cells producing IL-5 were counted, in triplicate, and the mean was taken to determine cellular response when stressed. The results were compared to determine if there is a difference between cytokine release amongst younger and older adults who experience TBI. By having a better understanding of how TH2 cell function is affected by age, we are exploring if overall outcomes following traumatic brain injuries are related to differential immune responses. This knowledge can potentially assist in identifying strategies to improve clinical outcomes.

Spinal cord injuries cause damage to the corticospinal tract which can lead to deficits in coordination and movement. This greatly alters and may decrease an individual’s quality of life. This project utilizes optogenetics to trigger action potentials in neurons, and tests the hypothesis that activity can promote regeneration of corticospinal connections. Co-cultured mouse spinal and cortical neurons serve as an in vitro model system. The spinal and cortical neurons are in separate chambers that are connected by a canal. Cortical cells are transfected with light- activated channels and stimulated with LED lights to trigger action potential firing. The canal connecting the chambers allows for the cortical neurons to form new synapses with the spinal neurons. In order to quantify the results, synapsin, a protein found in presynaptic vesicles, is labelled using immunocytochemistry, allowing us to quantify the number and size of synapses by measuring synapsin-positive puncta. It is expected that cells stimulated with light will show a greater number of synapses compared to those that were not. Different patterns of neuronal stimulation are tested to determine the best parameters for promoting synapse regeneration and strengthening. Once these have been determined, they will be validated in an in vivo rodent model, prior to testing in primates.

Synaptogenesis is the developmental process in which neurons form connections with their appropriate partners. However, the mechanistic bases for synaptic partner matching are largely unknown. To help address this gap in our knowledge about neural circuit formation, we are attempting to identify factors that drive specificity in synapse formation between nociceptive sensory neurons, known as Class IV dendritic arborization neurons (C4da), and their synaptic partners, A08n interneurons in Drosophila melanogaster. We hypothesize that C4da neurons express cell adhesion molecules that serve as specificity factors. Expressing such specificity factors in sensory neurons that do not normally synapse with A08n, for example C3da neurons, should drive spurious synapse formation with A08n. To test this, I used the split Gal4 system to develop transgenic tools for targeting gene expression specifically in C3da neurons. In this system the Gal4 transcription factor is split into its DNA binding domain (DBD) and activation domain (AD) which are independently expressed in overlapping cell populations and assemble to yield functional Gal4 only in cells that co-express both pieces. The complete Gal4 protein can then interact with UAS (upstream activating sequences) elements to drive gene expression. To develop a C3da-specific Gal4 driver I first engineered transgenes containing the Gal4-DBD fused to promoters predicted to be expressed in C3da neurons and other non-da neurons. I generated transgenic fly lines harboring these transgenes via direct injection of DNA into the fly germline. I then crossed these transgenic lines to a fly line that expresses the Gal4-AD element in C1-C4da sensory neurons. I expect to see functional Gal4 only in C3da neurons, which I can test by monitoring Gal4-dependent Green Fluorescent Protein expression. The resulting C3da neuron-specific driver will allow us to test whether ectopic expression of candidate specificity factors in C3da neurons is sufficient to drive synapse formation with A08n interneurons.

Infants born prematurely often suffer from hypoxia-ischemia and inflammatory responses that can lead to cognitive delay and behavioral problems. A novel rodent preterm brain injury model is being developed to simulate histological and behavioral changes seen in preterm brain injury. It was hypothesized that injured pups {in-utero hypoxia-ischemia followed by post-natal lipopolysaccharide (LPS)} will have a significant early behavioral deficit compared to controls. The rodent model of preterm brain injury includes: intrauterine hypoxia at embryological day 18, with postnatal LPS administration from Postnatal (P) day 2 to P4. In order to assess behavioral changes I conducted early reflex and motor skill tests on rat pups from ages P8 to P13. Early reflex testing included: righting reflex, negative geotaxis, and cliff aversion. Early motor testing included: ambulation, front limb suspension, hindlimb suspension, and grip strength. There was no significant difference seen in early reflex testing between control vs injured. Significant difference (P<0.05) was observed between control (n=19) vs injured (n = 11) in early motor testing: grip strength impulse, ambulation, hindlimb suspension and front limb suspension. Based on these findings, the novel preterm brain injury model is producing a motor deficit in the injured groups compared with the control group. Going forward, we will continue to repeat this experiment to verify the results and further elucidate what aspects of behavioral development are impacted most by this injury model.

Alzheimer’s disease (AD) is a debilitating neurodegenerative disease that currently affects >5 million individuals. We have previously demonstrated genetic and neuropathology-based variation across cognitively-defined AD subgroups. Here we sought to determine whether patterns of vascular risk factors differed across cognitively-defined subgroups. We used data from the Adult Changes in Thought (ACT) Study and the Religious Orders Study/Memory and Aging Project (ROS/MAP). These are prospective cohort studies of individuals who are dementia-free at enrollment. We used cognitive data at the time of AD diagnosis to determine scores for memory, visuospatial abilities, language, and executive functioning. We used these scores to determine each individual’s average cognition and then domain-specific deficits below that individual average. We used these data to define six groups: no domain with a substantial relative impairment; isolated substantial relative impairment in memory, in visuospatial functioning, in language, or in executive functioning, and multiple domains with substantial relative impairments. We evaluated risk factors for these six groups from self-report and/or diagnosis data on vascular conditions, including diabetes, stroke, hypertension, atrial fibrillation, cholesterol levels, and coronary artery disease. We used multinomial logistic regression models with the no prominent domain group as the reference. To account for multiple comparisons, we present tests of the null that each risk factor is unrelated to each subgroup, and an omnibus test of the association between each risk factor and any subgroup. The proportion of individuals in each subgroup differ between the two studies. Our results suggest possible differences in risk for specific cognitive domain deficits associated with stroke history, HDL cholesterol, and treated diabetes. Subsequent work will attempt to understand possible mechanisms behind these associations through literature review. These results support additional efforts to further understand cognitively-defined AD subgroups.

Building relationships with students may not be an easy task as a teacher, because students are coming in with a diverse range of differences which includes students’ backgrounds (i.e. life outside of school, race, socio economic status), perspectives, behavior, and interests. Teacher-student relationships may help increase student engagement, increase their sense of belonging, and help foster a safe environment which can have a significant impact on their success. Unfortunately, research has shown that many teachers are unprepared to teach students from diverse racial and cultural backgrounds. One reason may be that teacher preparation programs have not been as successful in changing teacher's values, attitudes, and dispositions related to teaching culturally diverse students. In my research, I examined the structure and content of the University of Washington Elementary Teacher Education Program (ELTEP) to better understand how teacher candidates transfer knowledge from their course work into their field placement, focusing on classrooms that are situated in culturally, racially, and ethnically diverse Seattle public schools. I analyzed how teacher candidates took up strategies for building teacher student relationships from their coursework into their field placements. I did so through interviews and ethnographic observations, analyzing teacher student communication patterns (i.e. one on one interactions, positive and negative reinforcement, humor, body language, etc.) in their field placements. My findings have significant implications for improving ELTEP coursework focused on building teacher-student relationships and ultimately improving student success in Seattle public schools.

Chronic pain is a perplexing and complex disease that may inflict physical disability or psychological impairment on individuals due to a medical illness or intervention, acute injury, or in the absence of physical illness or injury. Yet while chronic pain affects individuals across all age ranges, certain groups are disproportionately represented in chronic pain research. In particular, limited chronic pain research has focused on adolescents and young adults (AYAs) roughly between the ages of 16 and 25, leaving unanswered questions about how and when AYAs with chronic pain achieve developmental milestones such as gaining employment, forming romantic relationships, and living independently. The focus of this project is to investigate the effects of chronic pain on AYAs and aims to answer the following research questions: (1) Does the age of onset of chronic pain influence how AYAs achieve developmental milestones, (2) What developmental milestones are achieved by AYAs with chronic pain and how do they compare to controls who experience no chronic pain, and (3) Are commonly applied psychological measures ascertaining the most important information from AYAs? To answer these questions we performed a secondary data analysis of a data set of AYAs reporting to a tertiary pain center in the United Kingdom. This data set is courtesy of Dr. Hannah Twiddy of the University of Liverpool. Our analysis includes questionnaire data in the form of validated measures for impacts of pain on lifestyle, disability, depression, and self-esteem among others.  Results of this study describe the developmental milestones achieved by AYAs suffering from chronic pain and will help psychologists understand the nature of chronic pain in AYAs, and potentially develop more effective treatment plans in the future.

Homelessness among youth in Seattle’s University District has become a crisis that has been overlooked and neglected by our community. The lack of accessible resources and poor educational opportunities, have made it difficult for this population to have their basic needs met. A major resource homeless youth lack is a solid support system. This research project is part of a larger community project that is looking at the barriers that are inhibiting homeless youth from meeting their needs and escaping homelessness. The purpose of this study is to describe, from the youth’s perspective, the resources and support that are needed to help them achieve overall health. The larger study will design and implement a sustainable community café for homeless youth and youth at risk for homelessness in the University District that provides services and support. For this study, we applied a digital storytelling methodology, which is used as a community based participatory approach, to gain better understanding of youth homelessness and their needs in their own words. Digital storytelling is typically a short video 3-5 minutes long. The interviews were guided by questions as well as open conversation for the participant’s to share their story of homelessness. We conducted three interviews and created three digital stories. This study did not contain random sampling and was conducted strictly by a volunteer basis. After the interviews were conducted we used digital images with voice-over narrative to create the digital story. The aim was to analyze these videos to shed light on the specific needs the youth have. It also served to give researchers more information on the particular barriers homeless youth are currently facing and guided activities within the community café. These will also help suggest legal and policy reform in the homeless youth community as well as bring greater awareness to the community.

South Korea’s rapid industrialization and democratization led to policy reforms that allowed women to invest more heavily in their education, career, and leisure beyond the domestic sphere. Consequently, these women became active participants and consumers of the goods and services within their society, as exemplified by their consumption of media. Given that Korean women in their twenties and thirties have embraced strategies to improve their status as citizens who operate in society in ways that transcend traditional normative, restrictive spheres of action, we would expect them to explain their consumption habits in terms of how the cultural objects resonate with their own experiences. Instead, they reveal ambivalence with regards to the value of these dramas as accurate representations of Korean society. Why? I argue that the widespread consumption of Korean dramas replete with mixed messages that call into question these women’s self-fashioning aspirations can be explained as a function of their ability to detect and stand apart from the submissive qualities reflected in female characters whose behavior represents a capitulation to traditional gendered norms. Through open-ended interview questions about professional women’s viewing habits and career objectives, I demonstrate how the critical distance attendant upon drama consumption is an agentive coping mechanism beyond a passive act of acquiescence to gendered discrimination, and is premised on self-perceptions of critical acumen nurtured by their academic and vocational background. Such knowledge resulting from women’s intense focus on education derives from their perception of education as a conduit for the actualization of career aspirations, which equipped them to interrogate gendered power relations that pose challenges to their success. Critical acumen is viewed as the source of their capacity to recognize and distance themselves from popular media’s representation of gendered socio-economic inequality and the broader patriarchal discourse in Korea that perpetuates norms of women’s submissive position.

Dungeness crabs (Cancer [Metacarcinus] magister) hold commercial and cultural value in Washington State, yet little is known about the effects of climate change on their population--even less is known about their competitor, the graceful crab (C. [M.] gracilis). To investigate the effects of temperature and size on feeding rate, we conducted consumption experiments in aquaria at multiple temperatures and across a variety of sizes (70-100mm carapace width) of Dungeness and graceful crabs. We investigated their weight-specific feeding rates, egestion, and excretion via a basic mass balance bioenergetic equation in which consumption must equal respiration, egestion, excretion, and growth. We measured the egestion and excretion components of consumption by collecting unconsumed food material and fecal material, respectively. This multi-species comparison evaluates size and temperature-dependent feeding patterns that have implications for future spatial distributions and energy requirements of Dungeness and graceful crabs across Puget Sound. Future management of the fishery and ecological impacts under changing conditions are discussed.

Young people spend two-and-a-half as much time watching Internet videos as they do traditional television. Business concerns aside, questions remain about other effects of this change in media consumption. One such concern is of celebrities and their influence. Research demonstrates that celebrities are influential, in part because people consider them credible sources, even with regard to political information. Research also shows that a credible source is more effective at changing one’s attitude and behavioral intention than a low-credibility source. These research findings might alter what was previously perceived as the influence of traditional celebrities – movie stars, pop groups, and the entertainment industry as a whole. With the growth of particular participatory platforms and social media sites, a new type of celebrity exists: microcelebrity. Defined as an act of bolstering digital self-representation through media and technology, the term microcelebrity has since evolved to include individuals who construct self-representation and garner popularity online. Although there is a great deal of research demonstrating that microcelebrities are also influential, especially regarding consumer good purchases on social media, the question of microcelebrity influence on politics remains. In a two by two experiment, this study starts with a literature review on credibility, traditional celebrity, their political influence on audiences, followed by an introduction to microcelebrities and their influence, with a method section that leads to a few hypotheses. First, according to past literature, it is hypothesized that traditional celebrities are evaluated as more credible than microcelebrities. Second, male celebrities (both traditional and microcelebrities) are expected to be evaluated as more credible than female celebrities. Third, traditional male celebrities will be more credible than any other kind of celebrity. Given credibility is deemed by scholars as a crucial component of persuasion, assessing microcelebrities’ credibility provides a better understanding of their societal and political mpact.

Impella devices provide temporary mechanical circulatory support (MCS) by means of a catheter consisting of a left ventricular (LV) inlet, a microaxial pump within the catheter, and an outflow port in the proximal aorta. The recommended position of the inlet is 4-4.5cm below the aortic valve annulus. Following initial placement, the device is prone to migration, potentially leading to ineffective support, hemolysis, ventricular arrhythmia, or mitral regurgitation. Positioning is typically monitored by echocardiography. However, the Impella device has a bend between the inflow and outflow ports, and traditional 2D-imaging may not be reliable in assessing the location of the device, as single plane 2D windows may not include both the inflow port and the aortic annulus, leading to foreshortening of the cannula and under-measurement of the distance. We hypothesized that 3D echocardiography provides more accurate characterization of the Impella cannula location. We analyzed 25 echocardiograms of patients with Impella devices placed in LV which had analyzable 2D and 3D images. Measurements of the distance from the aortic annulus to the inflow port were made according to recommendations from established measurement guidelines. Three sets of measurements were made at end systole and at end diastole. Full volume 3D datasets acquired from the parasternal window were acquired an analyzed using Qlab software to overcome possible foreshortening of the Impella cannula. In addition, the 3D dataset was used to measure the angle deviation of the cannula from the long axis of the left ventricular outflow tract. There was no recognizable benefit of 3D techniques in measuring aortic annulus to Impella inflow port distance. A larger sample size may be necessary to detect a significant difference. 3D imaging may have a benefit in observing other relationships, such as the mitral apparatus, and bears ongoing investigation.

Staphylococcus aureus is responsible for large numbers of patient morbidity worldwide. However, studies of this important pathogen have suffered from the lack of a robust toolset for scalable genetic and genomic manipulation in the organism. Our goal for this study was to develop an efficient, simple, and inexpensive system for precision genome engineering in S. aureus. Our strategy employs ssDNA oligonucleotide recombineering coupled with CRISPR/Cas9-mediated counterselection to address these needs. We first identified a single-stranded recombinase protein, EF2132, derived from Enterococcus faecalis, which can successfully integrate single-stranded DNA oligonucleotides into the S. aureus genome. Our results showed that EF2132 readily mediates recombineering across many different laboratory strains and primary clinical strains, normally yielding thousands of recombinants per transformation. We proceeded to expand the generality of our genome editing system by incorporating lethal counterselection, enabling efficient recovery of recombineered isolates lacking a selectable phenotype. We constructed a temperature sensitive, two-vector system that enables conditional recombineering and CRISPR/Cas9- mediated counterselection in S. aureus without permanently introducing exogenous genetic material or unintended genetic lesions. Our findings indicate that our system effectively targets and edits genes with both specific mutations and large-scale knockouts by utilizing inexpensive, commercially synthesized oligonucleotides as substrates for inducing and counterselecting precise genomic changes. Since our system utilizes cheap synthetic DNA oligonucleotides as substrates for recombineering and counterselection, it provides a scalable, precise and inexpensive tool for producing isogenic strain in S.aureus. Because of this, our system can be used to effectively facilitate future studies to investigate the genetic mechanisms of many different biological phenomena. As our study progresses, we hope to introduce refinements to further improve the scalability and efficiency of this methodology.

Ethnic and religious violence on the border of western Myanmar’s Rakhine State and Bangladesh displaced approximately 647,000 Rohingya (residents), a stateless Muslim minority in Myanmar since August 25, 2017. The fact that this crisis has not been fully addressed by the Burmese majority is very alarming especially under the administration of Aung San Suu Kyi, the prominent political figure of Myanmar. Hence, the initial purpose of my research was to examine the factors contributing to this humanitarian crisis by conducting interviews, oral histories, and online surveys among resettled Rohingya women in the Greater Seattle area. I employed a transformative feminist theoretical framework to understand the relationships between political subjectivity and gender violence and colonialism, military dictatorship, and patriarchy. However, while recruiting participants for my project, I encountered silence and reticence rather than enthusiasm from the Rohingya community. This wall of silence and the absence of Rohingya community even among the small Burmese populations in Greater Seattle Area has been a significant turning point in my research. Perhaps this silence itself indicates Rohingya fears that even the researcher-researched relationship could expose them to further racism and discrimination from Burmese here in Seattle on top of their sufferings from political trauma and sexual violence in Myanmar. Therefore, I am currently implementing an auto-ethnographic approach to excavate the role my own and other majority Burmese immigrants' perceptions of and ways of representing the Rohingya, and how this has contributed to the current distrust, silence and fear between women in two communities who have both experienced sexualized military violence. By doing so, I hope my research will begin a process of facing Burmese internalized racism, sexism, and religious discrimination towards the Rohingya community and serve as the stepping stone towards inclusive community-building with cultural humility here and in Myanmar.

This project seeks to highlight and archive the lives, stories, and experiences of queer and trans people of color at the University of Washington. Queer movements have historically rested on the labor of queer and trans people of color, however, these histories are often whitewashed. The experiences of queer and trans students of color are not ones that are often archived or given space to be told. Through this project I seek to give space to stories and lives that are pushed to the side and silenced. I also seek to find commonalities among different yet similar student experiences. This project is based in one-on-one, in-person interviews with induvidual students. As an interviewer, I ask the interviewees questions about experiences include upbringing, familial structure, cultural context, coming into queerness, finding queer of color spaces in and outside of the university context, looking to the future, and ways of healing from traumas. My methods include in-depth audio and visual recorded interviews, and full detailed transcripts of each interview. As a member and leader of the Queer People of Color Alliance at UW, I am a part of and have access to queer communities of color at UW. This project highlights the importance of induvidual narratives, as they inform larger understandings of queerness and community. In addition, this project builds an archive of queer and trans student of color experienes that, among other things, highlight the importance of institutional spaces within the university campus that supports queer and trans students.

 The so-called DREAMers are the current generation of largely undocumented youth named after an unrealized piece of Congressional legislation known as the Development, Relief, and Education for Alien Minors or "DREAM" Act. These youth, many of college-age, are the source of an unrelenting voice for the advancement of immigrant, civil, and human rights throughout the United States. Their movement mirrors earlier struggles that resulted in significant social, economic, and political change; taking the form of direct-action protests and involvement with state, national, and transborder organizing campaigns through social media networks. This ethnographic research project explores the DREAMers' Movement in terms of activists' enunciations of identity, subjectivity, and civil disobedience in the context of the State of Exception created by the Trump Administration's engagement in biopolitics. I address the principal research questions: Are new radicalized political subjectivities emerging from the widely shared daily-lived experiences of precarity among the self-identified members of this movement? How does this subjectivity shape DREAMers' perceptions of and engagement with identity politics and civil disobedience in their rebellion against their status as bodies without rights? These questions were research through ethnographic methods, such as one-on-one interviews and participant-observations. Ultimately noting new forms of engagement in activism and the creation of new identities and ideologies surrounding civil disobedience, this project will provide a scholarly space for reflections on the DREAMers' Movement and its prospects for transforming national and transborder narratives of self, citizenship, and belonging in this political era.

The space program is a quickly expanding industry that promises trillions of dollars within the next 20 years. Countries are scrambling to cultivate space programs as the opportunities, both scientifically and economically, develop before our eyes. The United States leads the pack in the global space industry, and Washington State is a strong contender as front-runner in the US space program. With 26 federally recognized tribes, it is easy to see First Nations people being left behind in this lucrative business. How can we, as First Nations peoples, indigenize the space program by contributing our vast amounts of historical knowledge and re-appropriating the industry to reflect our unique views and histories? Do indigenous groups even want to be involved in the space program? And finally, how do tribal governments benefit from the financial benefits of the space program? By doing archival research of tribal views on space, the space program, conducting a field study based on the geography and economics of Spokane Tribe of Indians, and considering my own knowledge as a Native American identifying woman, I was able identify issues and formulate policy recomendations. Unfortunately, it is all too easy to see this important demographic becoming overlooked by this financially profitable opportunity. If First Nations groups will ever feel comfortable becoming part of the space program, their voices and sacred views need to be respected and valued. The US government also needs to make sure that indigenous people are able to have the opportunities that allow them to participate and share their views. Lastly, tribal governments need to find ways to indigenize the space program and make sure our communities see the economic profit that can be yielded from this extremely important industry.

Oral history projects documenting Japanese incarceration typically prioritize the stories of those that directly experienced the traumas of incarceration. Although trauma can be experienced by one generation, it can manifest and be passed down to subsequent generations through storytelling; trauma can also be experienced through silence, or the refusal to share stories surrounding a traumatic event, affecting individual and cultural identity. Very little scholarship has documented or closely examined the oral histories of those who did not experience Japanese incarceration themselves but have family members who did. The goal of this project is to examine the intergenerational communication of trauma and the cross-generational effects of Japanese incarceration on the Sansei generation (grandchildren of Japanese immigrants). Densho is an organization that documents and makes accessible through their online database the oral histories of Japanese incarceration experiences using digital video recordings and full written transcriptions of interviews conducted by them. I used digital video footage and interview transcriptions to qualitatively analyze for emerging themes or trends among the Sansei interviews surrounding how incarceration was communicated to them and its effects on them. I expect a common theme of emotional restraint and lack of communication of trauma among family members due to the impact of incarceration on identity and cultural practices. I also expect a trend among the Sansei interviews for seeking alternative means outside of family storytelling to learn about Japanese incarceration. Another result I expect is having their sense of cultural identity radicalized to seek justice for incarceration in varying ways. Placing significance on the generation of Japanese Americans who did not directly experience incarceration can further broaden the discourse of meaningful oral histories.

From November 2015 through March 2016, the Olympic Mountains Experiment (OLYMPEX) field campaign was conducted on the Olympic Peninsula to study how wintertime precipitation is modified as it passes over coastal mountains and to validate satellite-derived precipitation measurements from the U.S.-Japan Global Precipitation Measurement (GPM) mission. This project uses OLYMPEX data to explore the topographic effect on these Pacific frontal systems by examining cloud and precipitation structure on the leeward side (usually northeast) of the Olympic Mountains, where there is typically a minimum in precipitation relative to the windward side. While most research has focused on the structure of the windward side, this study uniquely examines the leeward side of the mountains. A radar managed by Environment and Climate Change Canada on Vancouver Island provided measurements of the vertical structure of the frontal systems over the northern Olympic Mountains, including intensity inferred from radar reflectivity. Using environmental data from NCEP North American Regional Reanalysis on the windward side (usually southwest) of the mountains, this study classifies the leeward radar data based on upstream synoptic conditions. It then examines the cloud and precipitation structure on the leeward side of the mountains in various atmospheric environments. Preliminary findings of this study reveal, for example, that the intensity of cloud systems on the leeward side is dependent on upstream stability. Locally, these findings will inform studies of snowpack and water supply as many reservoirs depend on precipitation that occurs on the leeward side. Outside of the Pacific Northwest, these findings can be applied to other midlatitude coastal mountain ranges on the west side of continents around the world.

Diatoms are small photosynthetic organisms that are important in global carbon fixation and help provide a base to the oceanic food web. Viruses are known to play a role in the overall life and death of diatoms but the extent of this role is not fully understood. A previous member of the Rocap laboratory has isolated a virus (PmDNAv) known to infect diatoms of the species Thalassiosira pseudonana. This virus is infectious in six out of the seven cultured strains kept in the lab; a seventh, CCMP 1012, is resistant. Each of the seven strains has a microbial community that propagates with the diatom cells as they are kept in culture. I hypothesized that the T. pseudonana CCMP 1012 was able to survive the viral inoculation because a beneficial microbe absent in the other strains was able to confer viral resistance. To test this hypothesis, I confirmed the previous results that showed viral resistance in the CCMP 1012 strain and susceptibility in another cultured strain. I then treated the diatoms with antibiotics to remove the microbial community. With the newly microbe free CCMP 1012 culture I performed infection experiments to test if the axenic strain would behave similar to the nonresistant strains and die, or if it would remain resistant to the virus. When the microbial community was removed from the previously resistant CCMP 1012, the strain was susceptible to viral infection. The most likely explanation was that the microbes were conferring resistance to the diatom strain. This implies that microbial interactions can lead to drastic changes in the dynamics at the base of the food web. Future work includes experiments questioning if the microbial community from the resistant strain can confer viral resistance to other strains and analyzing how the microbial communities differ genetically among resistant and susceptible strains.

Current studies have shown that changing climate is responsible for methane releases from the seafloor, making it important to understand how methane plumes can impact the ocean. Methane plumes impact the stratification and circulation within the water column which can influence primary productivity and seawater chemistry and potentially atmospheric greenhouse gas levels if the methane from the plume undergoes exchange with the atmosphere. Along the Washington margin there has been over 1772 individual bubble plumes located and identified in depths ranging from 40 meters to 1988 meters water depth. Compilation of archived CTD (conductivity, temperature, depth) data at active methane plume sites including Southern Hydrate Ridge, Grays Harbor, and Vancouver Island, can provide estimates of the plume fluids temperature and salinity. Using these estimates, the point where buoyancy reaches zero determines the possible depth of horizontal plume fluid intrusion into the water column and the entrainment coefficient to quantify the fluid that’s entrained by the plume can be calculated., I can determine the plumes’ ability to penetrate through sea water density interfaces such as the thermocline by calculating the Richardson number for the plumes. Using pre-established bubble models, I will also quantify sea water entrainment by the plumes. Through these methods, I will be able to determine how methane plumes impact water column stratification on the Washington Margin.

Viral infection is associated with asthma exacerbations. Normally, viral presence is detected by Toll-like receptor 7 (TLR7)—an innate immune receptor in airway epithelium that responds to single-stranded RNA viruses (like influenza) and triggers an immune response to infection. TLR7 is also expressed on airway sensory nerves, but its specific role is unknown. Here, I tested the role of TLR7 on sensory nerves and identified which sensory nerve populations express TLR7 using nerves isolated from dorsal root ganglia from female Hartley guinea pigs (~400 g). Ganglia were isolated, plated onto matrigel, and treated with a TLR7 agonist R837 (0.1-100 microM) for 16 hours. Neurite number per cell was not changed by stimulating TLR7, but neurite length, and the number of branch points were significantly increased. Separate experiments measured which types of sensory nerves expressed TLR7. Vagal and dorsal root ganglia were isolated and fixed in zinc formalin. Nerves were immunolabeled with antibodies against TLR7 and either neurofilament-1 (NF-H) to identify A𝛿 fiber sensory nerves or transient receptor potential V1 (TRPV1) to identify C-fiber sensory nerves. I found that airway sensory nerves originating in the vagal and dorsal root ganglia expressed TLR7. However, TLR7 was expressed predominantly on small TRPV1-expressing C-fiber neurons, but not on large NF-H-positive A𝛿 neurons. In conclusion, TLR7 is highly expressed by airway sensory C-fibers nerves, and its activation stimulates neurite growth. These findings suggest TLR7 may increase airway C-fibers supplying the lungs which may enhance airway reactivity and be a mechanism for virus induced exacerbations of asthma.

The catalytic activity of many metals can be increased when the catalyst exists as tiny nanoclusters as opposed to large bulk-like metal particles. Thus materials, or supports, that facilitate the growth of nanoparticle catalysts are highly desired. Of these supports, the most widely used are metal-oxides. The growth of catalysts on these supports can be better understood by studying the chemical bonding at the metal-oxide interface. The Mallouk group has found a calcium niobate nanosheet, HCa₂Nb₃O₁₀, that when used as a support both resists and reverses the coalescence of metal-oxide or hydroxide nanoparticles on the surface. These nanosheets are of additional interest because they are smooth on the atomic scale, similar to single crystal surfaces, with a large ratio of terrace sites to edge sites. Here, calorimetric measurements of the adsorption energies of silver and copper vapor on oxide thin films composed of four layers of these nanosheets are directly measured using adsorption calorimetry in ultrahigh vacuum. The initial heat of adsorption of silver atoms was found to be ~112 kJ/mol which closely resembles the predicted density functional theory (DFT) values for silver monomers. The growth mode of silver was determined using a surface sensitive spectroscopy technique, low-energy He+ ion scattering spectroscopy (LEIS). The number density of silver particles, as estimated from the LEIS data, was found to be ~2.2x10¹⁰ particles/cm² at 1.7 monolayer silver coverage. This is much lower than the particle densities on other metal-oxide supports and is attributed to the lower density of step/nanosheet edges on this support. The evolution of the LEIS signal indicates that silver grew as 3D nanoparticles. This data encourages further investigations of the adsorption calorimetry of different metals on this interesting support.

Patients and providers are beginning to use patient generated-health data (PGHD) to collaborate to understand patient routines, identify health problems, and tailor treatment strategies. However, current technology designs fail to support key aspects of collaboration, including planning, data collection, review, and analysis. Among all the health data people track, food data is essential for preventing and managing many health concerns. Although numerous tools exist to help people track and understand their diet and its consequences, these tools are often high burden, can lead people to focus on what is easily tracked rather than what is most relevant for their health, and fail to support effective collaboration between providers. In this study, we designed, developed, and deployed novel food tracking diaries to support healthy eating and the management of irritable bowel syndrome (IBS). Eighteen people with healthy eating goals used the food diaries for at least two weeks, and then worked with their health providers to plan changes to their diet. Sixteen IBS patients used the IBS version of the diary for at least nine days and then worked with providers to identify food triggers and plan changes. We interviewed patients and providers and observed their collaborations. The photo-based food diaries we designed supported patient-provider communication for both healthy eating and IBS. Compared to traditional food diaries, the photo-based food diaries make data collection, review, and analysis easier for patients and providers. However, patients and providers described scenarios when specific nutritional information -- beyond what they can see in photos -- helped the diagnostic or management process, such as when identifying IBS triggering nutrients. Our research will lead to better use of PGHD to give patients more tailored, accurate, efficient and informed treatment plans. Our results also inform the design of  food diaries that will better support people with different various health goals.

This research aims to examine the effects of nanoparticle-mediated inhibition of the phospholipid glutathione peroxidase (GPX4) pathway in mesenchymal state cells on radio-resistance in glioblastoma (GBM) therapy. GBM is a particularly deadly cancer with poor survival rates and relatively low treatment success, despite aggressive surgery and radiotherapy. Recent research has shown that biocompatible, tumor-targeted iron oxide nanoparticles (NPs) can serve to enhance radiotherapy through production of secondary electrons and subsequent reactive oxygen species (ROS) within the tumor volume. The presence of these NPs in the tumor during radiotherapy has shown to decrease damage to the healthy surrounding cells and prolong survival in mice with GBM tumors. This approach however, has not demonstrated the ability to eliminate the cancer completely, in part due to the presence of mesenchymal state cancer stem cells. The GPX4 pathway has shown to effectively kill mesenchymal state cells in sarcomas by inducing ferroptosis, an iron-dependent form of cell death. Here we plan to evaluate the efficacy of a range of GPX4 inhibitors on silencing of the GPX4 pathway and the ability to induce ferroptosis in primary human GBM cells. Inhibitors identified as effective silencers of the GPX4 pathway will be combined with a NP delivery vector to provide targeted delivery to GBM. The radioenhancement capabilities of iron oxide NPs in conjunction with targeted therapy against mesenchymal state cancer stem cells may provide a means to overcome radioresistance in GBM therapy.

The reduction of drug craving and subsequent relapse is central to the recovery process for individuals with substance use disorders. One of the goals of this project is to improve pharmacological treatment interventions for substance use disorders by better understanding how the neurotransmitter dopamine is involved in relapse. We investigated the relationship between drug craving and dopamine release in the nucleus accumbens core (NAC), an area of the brain that plays an integral role in reward-based learning and addiction, in male rats that have been trained to consume cocaine or alcohol. We tested the effects of L-DOPA, a chemical precursor to dopamine and a treatment that could reduce drug consumption, on craving and relapse-like behavior. Recent evidence from our lab suggests that decreased dopamine release in the NAC correlates with increased cocaine consumption in rats, and that L-DOPA administration attenuates drug intake. Preliminary data from our current project shows a similar effect of L-DOPA on alcohol or cocaine relapse. Our characterization of dopamine release in the NAC during both periods of drug abuse and withdrawal provides new insights for future studies and our use of innovative electrode implants for monitoring dopamine neurotransmission will pilot the technology for other drug self-administration studies. This will help to determine whether L-DOPA should be considered for treatment of cocaine and alcohol addiction in humans.

This research focuses on the mathematics of gerrymandering. Gerrymandering refers to how political parties draw district boundaries to give them better odds at receiving a majority during congressional elections. Every 10 years district boundaries in the United States are redrawn for congressional elections by the current majority party. With such change in political cartography, redrawing district boundaries not only affects who wins but also the people who live within them. Given the loosely defined criteria for redistricting, we seek to quantify the process of redrawing district lines to determine when this partisan process becomes an act of manipulation and exclusion. We will be use The Metropolis Hastings (M.H.) Algorithm to produce a random walk that has a stationary distribution that will be the probability distribution of all possible districting plans for a given U.S state. By collecting congressional maps and election results, we implemented the M.H. algorithm in python to produce sample spaces for Washington State and Iowa. We will simulate local and federal redistricting requirements using self-defined parameters which measure: compactness of districts, population division, division of counties, and minority voter populations. We simulated election results with respect to our sample districts and compared the simulated outcomes with actual district maps and their election results. This study helps to determine if current redrawn maps legitimately reflect the people they purport to represent or if they are manipulations and subversions of our democratic process.

Rhabdomyosarcoma (RMS) is a rare and devastating pediatric soft tissue sarcoma, predominantly diagnosed in children and adolescents. Metastases and disease relapse rates continue to remain poor with a 5-year survival rate of less than 30%. Current therapeutic methods continue to remain inefficient in causing complete remission. Cancer stem cells (CSCs), a subpopulation of cells within tumors, are able to resist standard therapeutic treatments leading to disease relapse and metastases. Studies using human cells and a zebrafish model of RMS has shown that a population of CSCs exists within RMS. Thus, I am interested in characterizing potential genes that serve as a marker for CSCs in RMS. I am currently pursuing two candidate genes called PAX7 and CD82. Both PAX7 and CD82 have been demonstrated to play an essential role in regulating the function of skeletal muscle stems cells. The molecular signature of the CSCs in RMS is similar to that of skeletal muscle stem cells. Our preliminary data in the Chen lab also demonstrated increased expression of CD82 in a sphere assay, a surrogate in vitro assay to assess stem-like features in tumor cells. Based on these findings, my central hypothesis is that PAX7 and CD82 can potentially serve as specific markers of the CSCs in RMS. To test the hypothesis, I tagged PAX7 and CD82 with the aid of the CRISPR/Cas9 genome editing technology in order to isolate populations of RMS cells that either express PAX7 or CD82. I will perform cell-based assays in order to assess whether the stem-like qualities are enriched in isolated PAX7 and CD82-labeled RMS cell population. The identification of the CSCs in RMS will provide insight for a novel solution in overcoming drug-resistant RMS, tumor recurrence, and metastasis, through CSC-targeted drug therapy.

With the growth of the internet, social networking sites have become an important part of relationships. A preliminary literature review has found post-dissolution distress is positively associated with online surveillance. Limited research has been done in understanding if breakup distress can predict post-dissolution online surveillance on other platforms. Therefore, systematically investigating the relationship between post-dissolution online surveillance and distress among young individuals will fix this gap in knowledge. As there has been a contradiction of gender as a predictor of breakup initiation, this study will also look at gender difference and breakup initiation as predictors of post-dissolution distress. There are three hypotheses in this study. H1: There is a positive relationship between post-dissolution online surveillance and post-dissolution distress. H2: There will be a statistically significant difference in distress between male and female. Female will experience more post-dissolution distress. H3: There will be a statistically significant difference in post-dissolution distress between those who attribute the breakup to their partner and those who initiate the breakup. Those who attribute breakup to their partners will experience more post-dissolution distress. This study will go under IRB review shortly and data collection and analysis will be conducted in April. The long-term goal of the research is to provide positive insights to human use of social networking sites and emotional health. Results of this project will ultimately help young individuals further their personal well-being.

Multiple factors interact to determine the lifespan of an organism. The Promislow lab uses the fruit fly Drosophila melanogaster to study the interaction between the metabolome (the profile of all small molecules within an organism), and the lifespan of a fly under stress. In a study of metabolome and lifespan data for many genotypes of Drosophila, our lab found that fly strains with relatively long lifespans when exposed to oxidative stress (peroxide food), had high levels of maltose, a disaccharide of glucose. We hypothesized that maltose was beneficial to flies on peroxide food, and tested this by supplementing the diet with maltose to see if this would extend lifespan. Flies fed supplemental maltose prior to exposure to peroxide food lived longer than flies fed unsupplemented food, supporting our hypothesis. Maltose could extend lifespan by providing energy to the fly via metabolism into glucose, or through another function as a disaccharide. To distinguish between these possibilities, we tested lactose, a disaccharide, to determine if any disaccharide could extend lifespan. Lactose did not extend lifespan, suggesting that disaccharides in general do not extend lifespan under stress. We found that glucose extended lifespan, supporting the hypothesis that maltose extends lifespan via conversion to glucose. Maltose can be stored as glycogen, a polysaccharide, and glucose is derived from glycogen by glycogen phosphorylase, encoded by the gene GlyP. To test the role of glycogen metabolism on lifespan under stress, we manipulated the expression of GlyP. Several transgenes were used to reduce the expression of GlyP by RNA interference (RNAi). RNAi of GlyP decreased lifespan, which supports our hypothesis that glucose derived from glycogen promotes survival. Our work suggests that glucose derived from glycogen or maltose is an important determinant of lifespan under stress, furthering our understanding of links between metabolism and complex phenotypes, like lifespan.

This research focuses on obtaining a better understanding of people’s knowledge regarding the US Civics Test or more commonly known as the Citizenship Exam. The US Citizenship Exam is taken by individuals who are in the process of becoming US citizens, meaning naturalized citizens. The purpose of this research is to survey individuals of different documentation status about their knowledge regarding the US Citizen Exam in order to obtain a better understanding of people’s interpretations of citizenship and Americanness, and to observe the correlation between key demographics and participants' beliefs. This research was conducted through an interview of 15 participants. The survey used to interview participants comprised of three parts: 1) demographic information about participants’ backgrounds, 2) five questions from the US Citizenship Exam, and 3) five conceptual questions about citizenship. This meant observing if participants knew the correct answers to questions from the Citizenship Exam, or were knowledgeable about the process to become a US citizen. Through the responses to the conceptual questions about citizenship, we obtained a better understanding of participants’ interpretations of citizenship and Americanness. With this data, we observed correlations between the demographics (identities) and the results (knowledge and beliefs). As a result, we find that the US Citizenship Exam neither efficiently nor accurately captures the meaning of citizenship. In addition, we also find that citizenship is not synonymous with feelings of being American. One may have legal status but may not feel American, while one may feel American and not have legal status. Overall, the findings complicate the concept of citizenship, and question about what it means to be American.

Non Hodgkin Lymphoma (NHL) affects over 70,000 people in the United States each year. Inappropriate activation of B-cell receptor signaling is associated with NHL, and therapies that target this pathway are showing promising results in the clinic. One example is ibrutinib, a small molecule inhibitor of Bruton’s Tyrosine Kinase (BTK). While ibrutinib has improved the prognosis for the majority of NHL patients, many patients eventually develop resistance to ibrutinib due to mutations in BTK and its downstream target Phospholipase C gamma 2 (PLCG2). Thus, it is important to understand how these mutations affect cell signaling, with the ultimate goal of designing new strategies to mitigate ibrutinib resistance. Previous studies in the James Lab suggest that long-term treatment of cultured cell lines with ibrutinib leads to increased cellular reactive oxygen species (ROS). However, it is unclear if ROS contribute to ibrutinib resistance or if they are a byproduct of other mechanisms that drive resistance. I hypothesize that cells with mutations commonly seen in ibrutinib-resistant patients may also exhibit increased ROS, and these cells may be sensitive to small molecules that regulate ROS. In order to test this hypothesis, I used CRISPR/cas9 gene editing with homology-directed repair to generate lymphoma cell lines that express a leucine-to-phenylalanine mutation in PLCG2. This is a well-described mutation in ibrutinib-resistant patients. Preliminary analysis shows that these mutant cells are resistant to ibrutinib. I measured ROS in these cells by ROS-Glo luminescence. Then, I cultured the cells with ROS-regulating compounds including SOD-1 and NADPH oxidase inhibitors to assess how ROS affect their viability. My goal is to clarify the role of ROS in the acquisition of ibrutinib resistance. These studies may provide justification for further pre-clinical evaluation of small molecule regulators of ROS in lymphoma, especially among subjects with acquired ibrutinib resistance.

Fluid mixing is big business, both its application and research. Many manufacturers must be able to reliably mix fluids to a satisfiable level of homogeneity. Fluids taking longer to mix are fluids not being used for their intended purpose. This research explores two specific uses of random processes in an attempt to increase the speed and/or quality of the mixing process. While most mixing processes are in practice deterministic, the ansatz of this inquiry is that fluid mixing may be better applied through randomness. In this research, two different models for fluid mixing are explored, implemented and statistical measurements are taken. The first is the Gather and Spread model proposed by Diaconis and Pal in 2017, the second is the Toroidal Lattice Mixing model proposed by Pierrehumbert in 2000. We calculate Kendall’s τ (tau), and show evidence for a linear relationship between the number of points in the Gather and Spread model, and the number of trials. We show evidence against Gather and Spread distributing its points in Poisson manner. We calculate the standard deviation and relative entropy in the Toroidal Lattice Mixing model. We find strong evidence for the TLM having an exponential mixing rate, and strong evidence suggesting that advection diffusion mixing methods are always faster than diffusion alone.

Cas9 has long been used as an effective genome-editing tool for its ability to knock out genes with high efficiency; only in recent years has it been used to activate genes as well. Our current research aims to develop Cas9 as a gene activating tool in zebrafish, and to use that tool to target genes associated with rhabdomyosarcoma, a devastating pediatric cancer, in order to better understand the genetic factors and interactions leading to tumor growth and progression. When a dead form of Cas9 is used (dCas9), it will bind to the specified site without cutting/knocking out the gene. We have developed a gene-activating system using dead Cas9 fused with a transcriptional activator (dCas9-VPR), and are currently optimizing its use with Csy4 in order to activate multiple genes in a pathway or genetic network. We have seen low efficiency success so far by injecting zebrafish with DNA coding for Csy4, dCas9-VPR, and guide RNAs downstream of the ubiquitin promoter. Once the system is optimized, we hope to use it to test interactions between multiple genes simultaneously, which would allow us to determine how interactions between genes impact cell behavior.
This will allow us to gain a more wholistic understanding of how a genetic pathway works.

Zika virus has become a major epidemic around the world due to the serious birth defects that it can cause; this has led to an increase in research regarding Zika and how to diagnose the disease. Diagnostic tests require a specific sample type to be tested for the presence of a virus, and because it has been shown that Zika viral levels are more consistent and reliable in whole blood compared to plasma or serum, whole blood is the more efficient sample type. Current strategies for diagnosing Zika fall short because there is limited data on how the virus presents itself in the body, and many of these strategies utilize expensive and time-consuming methods that are not feasible in low-resource settings where Zika is more prevalent. Therefore, there is a need for a low-cost and instrument-free process that can effectively purify Zika virus RNA from whole blood in order to allow for detection of the viral RNA. This project dealt with optimization of an existing lab protocol that required laboratory equipment and resulted in low efficiency. The aim was to develop a robust, high-efficiency, instrument-free RNA purification protocol for whole blood samples. The method of RNA purification consisted of a lysis and binding buffer, followed by RNA purification using silica beads embedded in paper to extract pure RNA from the sample. qRT-PCR was then used to quantify the resulting RNA. So far, the paper-based extraction method recovers approximately 20% of the initial target RNA; however, there are still some techniques that will be employed in the future to help improve this recovery rate. The goal of this project is to increase RNA purification efficiency and to provide an alternative mechanism to purify nucleic acids that can be used in a Zika virus diagnostic test.

Recent advances in RNA sequencing and molecular biology has allowed them to be at the forefront of diagnostic care. Although sequencing costs have decreased, existing methods for detecting gene expression levels are not feasible in a clinical setting. Creation of a simpler molecular diagnostic based on measuring gene expression levels in blood could provide an alternative as a reliable, fast and easy to perform diagnostic. Multiple genes can have various expression levels across patients and patterns of this differential gene expression is key in studying multiple diseases including cancer or autoimmune disorders. Before testing the platform with clinical samples a smaller classifying circuit that fluorescently differentiates between a series of different cancer cell lines was created. Directly, my work has been developing fluorescent reporter probes that will be able to categorize weighted genes in our classifiers neural network. Positive and negative gene weights can be used to differentiate between cancer cells lines as cells express certain genes in varying amounts between populations. When running samples in our qPCR protocol, addition of the fluorescent probes, allows each gene to be sorted into distinct fluorescent channels. After testing the probes using RNA extracted from our cancer cells (HEK, HEPG2, MCF7) results were similar to the known gene expression data when measuring a series of 5 genes across these cell lines. Additional, experiments are currently underway to establish a gradient for fluorescence so that not only the type of cancer cell can be determined, but the proportional amount with high specificity and low variability. After development the fluorescent probe system will be incorporated into a clinical sample protocol and the platform will undergo further optimization for clinical applications. For patients a novel diagnostic platform allows for a more thorough disease screening, longer treatment time and hopefully a more positive prognosis outcome.

Microglia are the resident immune cells of the CNS and are hypothesized to influence aging in the brain. Like somatic cells, microglia can be replaced by self-renewal. Recently, some studies have suggested that new microglia derive from asymmetric cell division of a progenitor population. Microglia progenitor cells have been difficult to study due to a lack of specific molecular markers of this population. However, the Garden lab has recently identified novel candidate markers. We hypothesize that in neurodegenerative disorders associated with advanced age, microglia progenitor senescence may contribute to disease pathology. To efficiently study the senescence of microglia progenitors, we turned to neonatal mixed glia cultures, in which the presence of microglia progenitors has long been inferred. In these cultures, microglia are harvested from cells floating above a monolayer culture of mixed neonatal glial cells. The size of each microglia harvest generally decreases with successive harvests. This suggests that microglia progenitors in the attached monolayer may become senescent after multiple rounds of the cell cycle, leading to stagnation in the generation of new floating microglia. We evaluated microglia progenitor senescence in neonatal mixed-glia cultures by labeling with BrdU, a thymidine analog taken up by proliferating cells and remaining in their daughters. Microglia harvested from these cultures weekly were assessed for BrdU incorporation using flow cytometry and immunofluorescent microscopy. We co-labeled floating microglia and dissociated monolayer mixed glia cultures with antibodies directed against a progenitor marker (CD133), a microglia marker (Iba1), and BrdU. The attached mixed-glia cell layer was also labeled for SA-ß-Gal, an indicator of cellular senescence. Progenitor senescence will be detected by a decrease in CD133/BrdU-positive cells and an increase in CD133/ SA-ß-Gal positive cells.

Organic electronics have generated wide interest and excitement because they are relatively inexpensive to produce and are created from abundant resources, unlike their inorganic counterparts. Many organic materials also possess the unique potential of being stretchable in electronic applications including solar cells, OLEDs, and transistors. These materials can be made into wearable electronic devices and have the potential to power other advanced technology. Organic electronics are often made using semiconducting polymers. However, these polymers are semi-crystalline and brittle in solid state. To enhance their stretchability, our approach is to incorporate stretchable rubber into the semiconducting material by chemically linking the two polymers to combine their properties. This research investigates the crosslinking the well-known semiconducting polymer P3HT, poly(3-hexylthiophene), with polybutadiene (PB), a common rubber, to create a stretchable semiconducting material. To make crosslinking possible, we synthesize P3HT that includes a functional bromine to produce P3HBrT, poly(3-(6-bromohexyl)thiophene). Once the P3HBrT is synthesized, it can then be crosslinked with PB at different ratios to optimize for conductivity and stretchability. The crosslinked P3HBrT/PB can then be made into a thin film transistor and characterized for the desired properties. Ultimately, future research in this area will lead to a new generation of electronic devices with improved material properties.

One issue in many medical applications is detecting the presence of forced exhalations or breaths through audio data. For example, analysing sleep disorder breathing or analysing a person's lung function from audio of their exhalation first requires localization of a breath event in an audio file. Past work has focused on extensive feature extraction from sound and machine learning methods to detect these events. However, these black box methods require significant feature engineering dependent on the type of exhalation and environment the audio data is recorded to find the start and end of an exhalation event. We present a novel method for detecting the start and end of forced exhalations for spirometry, a medical test of lung function, in audio files. The algorithm requires an initial set of audio files containing exhalations to be manually labelled for locations where exhalations can be heard. Then, we build an envelope which encapsulates the shape of our exhalation signal. We take the cross-correlation of this initial envelope with vast amounts of unlabelled audio data containing exhalations, and use the estimated locations of exhalation events to recalculate the envelope. We repeat this process with the new envelopes until convergence. The converged envelope is then used to autocorrelate an audio signal to detect the start and end of exhalation. While preliminary results show that this method only achieves comparable performance to ad-hoc approaches currently used compared to human labels, it has the benefit of being simpler and more interpretable, enabling easier improvements and runtime of the algorithm.

Headaches are debilitating conditions that can impose a severe drop in quality of life and productivity. Local anesthetic blocks of the greater occipital nerve (GON) have been shown to reduce pain in various forms of headaches that are resistant to conservative treatment. We are performing a quality improvement project on GON blocks in different forms of headache. One aspect of the project is to evaluate whether the block affects the area of referred pain. We analyzed 12 patients undergoing a GON block at the Center for Pain Relief of the University of Washington Medical Center. Bupivacaine 0.25% was injected under ultrasound guidance. Before and 30 minutes after the injection, patients drew their pain localization on a high-resolution 3D body schema on a computer tablet. Pain area was quantified in terms of number of pixels. 30 minutes after the injection, the patient’s global impression of change was recorded. The data were analyzed by paired t-test. The median pain area (interquartile ranges) prior to and 30 minutes after the procedure was 622,271 pixels (158,216-795,912) and 104,961pixels (27,466-448,391), respectively (p=0.0277). Analysis of global impression of change in pain showed 2 of the patients experiencing very good improvement, 3 good improvement, 2 minimal improvement, 2 who had no change in perceived pain, and 3 whose pain minimally worsened. GON blocks reduce the referred pain area of patients, pointing to potentially significant benefits of the procedure for patients suffering from headaches. However, the qualitative marker of patient impression of change shows that GON block efficacy may vary significantly on a case-by-case basis.

Paper fluidic devices expanded diagnostic medicine to applications beyond lab testing. A key example is the common pregnancy test, which relies on an antibody capture line and detection antibodies conjugated to a colorimetric label to provide a diagnostic readout. This detection method requires high concentrations of target proteins. However, by incorporating isothermal strand displacement amplification (iSDA) and antibody capture of proteins tagged with nucleic acids (rather than colorimetric labels) much smaller protein concentrations can be detected. The Yager Lab has shown that this method increases sensitivity by 10⁴ in comparison with conventional lateral flow methods. Incorporating iSDA into a multistep fluidic device poses the challenge of transporting, delivering, and holding solutions with accurate concentrations of iSDA reagents in an amplification region for thirty minutes. A specific difficulty is delivering the flow of rehydrated iSDA reagents and subsequently stopping fluid movement over the protein capture region. My initial work has been focused on designing and optimizing a device with stopped flow to create ideal amplification conditions evaluated with fluidic dye testing. By using fluorescein and ImageJ analysis to iterate device and membrane design, correct concentrations were delivered to the amplification region. To further the device automation, timers were incorporated so the only user step would be inputting the sample. The device then isolated the target protein, amplified the signal, and provided a diagnostic analysis for the user using a fluorescent probe. Such an advancement can further the reach of higher sensitivity protein diagnostic technologies to low resource settings and for in home testing.

Ultrasonic transducers are key components in the probes of ultrasound devices used for medical imaging. The probe consists of 4 different materials; a piezoelectric element, backing material, an acoustic matching layer and an acoustic lens. The properties of these materials will directly impact the performance of the transducer and the quality of the images produced, making them a high priority for future development. Currently, researchers at Siemens Healthineers are looking to develop new materials for our ultrasound probes to help increase device performance and make better ultrasound devices. This senior capstone project looks to develop the Acoustical Properties Measurement System (APMS), a characterization testing system, to aid in the production of the new transducer materials. Development of new MATLAB and LabView code has been carried out to provide a smoother operating experience and enhanced design simulation. Data storage has been revised to provide a single location for users to access all collected data and a new naming system has been implemented for easier sample tracking. A standard operating procedure has also been established to help aid new users in operation of the system and a new method for measuring high attenuation materials has been developed. These improvements to the APMS system will further benefit the research and development of Siemens Healthineers ultrasound devices, providing customers and their patients with provide accurate diagnoses and help them to make the best decisions for their care.

There is low economic incentive to pursue treatment and cure research and development for rare diseases; this leaves millions of patients living with rare diseases understudied and undertreated. With the inception of groups such as the Undiagnosed Diseases Network (UDN) there is now a wealth of rare disease patient data. One way to increase the number of diagnoses, and hopefully treatments, would be to use the data already available to identify disease causing genes and potentially treatments as well. It has been shown that the integration of network-interaction and genetic data can further our understanding of disease pathways and genes. We investigate how to unify rare disease patient data from sources like UDN and Protein-Protein Interaction (PPI) data to identify potential novel gene candidates on the individual patient level. We developed a pipeline integrating patient genetic data and PPI that shows promise in identifying novel disease genes. For one of our patients, our pipeline predicted a very compelling disease gene and their clinician was notified of our finding. In other cases, no disease genes were identified. These findings suggest that our pipeline shows promise but further optimization and validation are necessary. As more data becomes available and sequencing technologies become more inexpensive, we hope that our pipeline will be more accessible and find use to undiagnosed patients and their clinicians around the world.

At the 2017 Undergraduate Research Symposium, I presented a low-cost, automated device for influenza detection that was being developed in the Yager lab. After creating, testing, and optimizing this device, we were left with many questions. While certain components of fluid flow in paper are understood, there is much more to learn. In this device alone, three different types of paper were used to run the two-dimensional assay. Current unanswered questions include the following: how do additives affect protein deposition, rehydration, and capture? How much of a dried protein on paper can be rehydrated by a passing solution, and which paper and solution properties affect this value? How do the viscosity and complexity of our patient samples affect the quality of our results? Our overall goal is to determine how to optimize our test line and generate a better understanding for optimization of future diagnostic devices. To make progress towards this goal, my project centers on the development and characterization of a laboratory technique to quantitatively study the effects of these parameters on protein interactions with membrane surfaces and other proteins bound to those membrane surfaces. Improving our understanding of these interactions in membranes will enable better diagnostic device optimization and enable illness detection with lower amounts of infected sample – allowing for earlier detection and better disease treatment. Through the development of this testing apparatus, I have begun to address these questions.

Lateral flow tests are assays conducted on porous media, commonly referred to as paper, that can detect and quantify analytes in a sample. They have the potential to return results within minutes and can be used in low-resource or non-medical settings. Protein adsorption is critical in these tests because protein interaction with a media can affect the delivery of reagents or choice of blocking agents to prevent nonspecific binding. A computational model of the fluid and adsorption physics may improve the development of paper-based assays. Yet-to-be-published data from the Yager group evaluates protein adsorption based on the deposition and analysis of protein spots on paper. The computational model used is derived from Darcy’s law, commonly used to model fluid flow in porous media and to calculate volumetric flow rates. This model makes two main assumptions: the porous media is fully saturated, and there is zero outflow on the boundaries of the media. These assumptions are not applicable because the protein spot dries as a result of evaporation, creating a non-zero outflow at the surface of the paper. The saturation level in the paper will also vary therefore Darcy’s law is not an adequate representation of the paper. My project aims to develop a more accurate computational model of fluid and protein absorption dynamic by modeling protein spots on paper. I incorporated an evaporation component that will allow the use of Richards equation to model fluid flow, which applies to unsaturated conditions. This is coupled with a protein transport and adsorption component to achieve a complete model. Although literature on evaporation from sand or soil is abundant, these results cannot be directly applied to evaporation from paper. This model will aid the diagnostic community in better understanding their assays and ultimately help improve the sensitivity and specificity of their assays.

Study of the thermodynamic properties of pure water and aqueous salt solutions of NaCl and Na2SO4 were undertaken to determine the equations of state for ices VI and VII at pressures from 1 to 4 GPa and temperatures from room temperature to approximately 300 ℃. The analysis was performed on data along the melting curves of pure water and aqueous solutions of up to 4 mol/kg of Na2SO4 and NaCl as measured within the pressure chamber of a Diamond Anvil Cell (DAC) utilizing ruby fluorescence spectra as a pressure gauge. The data were fit using a local basis function representation, allowing the comparison of the melting surfaces for the two salt solutions over a range of concentrations. Equations estimating evolution of the liquid-ice VI-ice VII triple point with increasing salt concentration, and prediction of the eutectic were enabled from the fit, providing better constraints on structural and geodynamic modelling of icy worlds. Melting point depression with increasing concentration of salt and incorporation of the salt ions into the crystal lattice, and density inversion between the high-pressure ices and saline solutions suggest the possibility of deep oceans of alternating layers of water and ice. Quantification of the effects of aqueous salts on these ices will allow the development of realistic modelling of the hydrosphere of icy worlds and exoplanets. Such modelling can be used to test the possible existence of chemical composition and water/rock dynamics favorable to the existence of habitable zones in these extreme environments.

The goal of this research is to improve breast cancer treatment by identifying novel imaging markers of tumor immune response. New immunotherapy treatment approaches are emerging that harness the body’s own immune system to fight cancer. These exciting advances increase the need for new tools to quantify response and assess treatment effectiveness in vivo.  We are investigating the potential role of magnetic resonance imaging (MRI) in monitoring chemotherapy-induced immune response in breast tumors. HER2 (human epidermal growth factor receptor 2) is a protein overexpressed in up to 30% of breast cancers that can increase cell proliferation and result in more aggressive cancers with worse outcomes. Trastuzumab is a drug that has been shown to not only amplify, but also induce immune response in HER2+ tumors. This induced immune response contributes to the effectiveness of trastuzumab in fighting HER2+ breast tumors and improving overall survival.  We hypothesize that functional MRI measures can identify changes associated with tumors’ immune responses. We are testing this hypothesis preoperatively in a group of patients with HER2+ breast cancer. Each patient has an MRI image taken and a tissue sampling of their tumor before and after a dose of trastuzumab. Quantitative MRI metrics we are measuring include contrast enhancement kinetics reflecting vascular permeability and diffusion coefficients reflecting tumor cellularity. Changes reflected on MRI are being compared with changes in histologic measures of immune response (including tumor infiltrating lymphocytes, TILs, and inflammation). Objectives are to identify quantitative MRI markers that are best suited to track breast tumor’s responses to trastuzumab. These findings are contributing to developing a novel method of observing immune response in tumors treated with a variety of emerging therapies.

American Indian / Alaskan Native communities are asserting their rights as sovereign nations to integrate culturally relevant practices and community-wide protections into research that is conducted within their Nations. Institutional Review Boards are entities responsible for overseeing all research that involves human subjects and ensuring that ethical standards are met. This work seeks to examine the similarities and differences between Tribal Institutional Review Board (IRB) and Non-Tribal IRB application processes.  We compared six Tribal IRB applications created by three different tribal communities, one tribal college, one tribal health organization, and an Indian Health Service Area Office. The major contributions of this work include a dataset of all federally registered tribal IRBs, a systematic analysis of the difference in online presence and format for application requirements, and a better understanding for the unique place-based requirements central to tribes. Preliminary results include a new dataset of 33 active and 17 deactivated federally registered Tribal IRBs. Our comparison of six of these active Tribal IRBs has revealed notable areas in which they are similar to each other and different from Non-Tribal IRBs.  These areas include community involvement in the research process, ensuring research meets communities' needs, awareness and implementation of culturally respectful methodologies, meaningful reporting of results to the researched communities, and tribal ownership of research data.

Enteric diseases, or diseases of the Gastrointestinal (GI) tract, remain one of the most prevalent killers of children in sub-Saharan Africa. The most practical way to prevent such diseases is through vaccination, but antigens for enteric diseases need to be delivered directly to the GI tract to be most efficient, making vaccination difficult. Recent studies by the von Adrian group at Harvard University have found that both T and B cells are reprogrammed to home to the GI tract when they encounter retinoic acid, a metabolite of vitamin A. The King Lab at the University of Washington is working to develop a novel vaccine candidate using recently developed self-assembling protein nanoparticles, that can simultaneously package all-trans retinoic acid (ATRA) and multivalently display enteric antigens. Recent data indicate that preliminary versions of these nanoparticles can successfully elicit a mucosal immune response when delivered with free ovalbumin, an avian egg protein that is frequently used as a model antigen. We expect to elicit more potent immune responses when the antigen is multivalently displayed at high density on the nanoparticle. To accomplish this, I created a library of plasmid constructs combining ovalbumin and several nanoparticle subunits using a variety of different linkers. I expressed, purified, and evaluated these nanoparticles for their expression of the antigen using enzyme-linked immunosorbent assays, or ELISAs.

There is a health crisis of unusually high rates of suicidal ideation, alcohol abuse, and other problems of identity and, in turn, mental health among Filipinx Americans today. These indicators of individual and community suffering can be attributed to historical trauma—a concept initially used among Indigenous scholars to describe the psychological trauma and other embodied impacts of centuries of colonization and oppression—which in the Philippines, has meant colonization by several nations and the ongoing imperialism and military presence of the United States. Outside of traditional healthcare, music culture has provided Filipinx Americans a safe space for healing, resistance, and resilience through creative expression and identity development. In the face of US imperialist policies, racism, and other oppressions, Filipinx Americans have had significant contributions to music culture and radical political movements that largely go underrepresented in US history and contemporary studies, including Seattle’s rich narratives of social justice and art. As a self-identified Filipinx American queer femme, DJ, artist, and social justice advocate, I conducted oral life histories and collaborative art projects among Filipinx musicians, artists, activists, and community organizers. Preliminary findings suggest several themes, including (1) relations between Filipinx American music culture, identity development, and health; (2) sociocultural anthropology research’s potential to support radical political movements for Philippine independence and collective liberation; and, (3) the role collectivism can play in building power among Seattle’s Filipinxs and people of color and their art scenes, so that we may compensate and duly recognize the city’s marginalized communities. This work advocates for anti-imperialist action among Filipinx artists and activists through a framework of personal healing, community relationships, and collective movements for justice. Overall, my research supports my journeys of identity, health, and art alongside ongoing legacies of music as a significant political resistance tool in Seattle and the greater Filipinx American diaspora.

Hip hop is both a globalized movement and culture that gives marginalized community members an outlet to express themselves creatively. The hip hop community posits itself as one that welcomes individuals based on one’s credibility through the four pillars: rapping, DJing, breakdancing, and graffiti art. However, despite the “openness” the industry pushes forth, an individual’s race and gender, especially not being a Black, heterosexual male, complicates one’s access to opportunities. Asian Americans, in particular, must simultaneously subvert and reclaim their identities from controlling ideologies through their navigation of hip hop. In this study, I conducted a semi-structured focus group with Asian American hip hop artists from the greater Seattle area (all ranging in age). I conducted individual follow-up interviews with participants, utilizing a narrative inquiry methodology. The combination of the focus group and individual interviews enables me to outline the richness of participants’ hip hop experiences. My preliminary findings indicate that Asian Americans must not only face impositions by mainstream media outlets but also within the liminal spaces of hip hop. Renegotiations and reaffirmations of identity prove critical for Asian Americans because they correspond to a liberation from racialized and gendered scripts. Moving forward, one implication of this study is the limited scope of Asian ethnic representation within all four of the pillars of hip hop, and the need for Asian Americans to redefine themselves within hip hop.

Ovarian cancer is the deadliest of gynecological malignancies, with approximately 70% of patients diagnosed at an advanced stage of disease. With the current standard of care, cytoreductive surgery plus chemotherapy, the relapse rate is about 70% and the 5-year survival rate is less than 50%. Innovative therapeutic interventions are greatly needed, and one promising new strategy mimics the body’s endogenous anti-cancer immune response. This immunotherapy approach uses donor T cells engineered to express a T cell receptor (TCR) that is specific for a tumor-expressed antigen. Mesothelin (MSLN) is a validated antigen target, frequently over-expressed in cancer cells compared to healthy tissues. Using the mouse ID8 ovarian tumor model, we found that T cells engineered to express a high-affinity MSLN-specific TCR can kill ovarian cancer cells. However, the T cells lose effector function over time, which correlates with increased expression of the T cell inhibitory receptors PD-1, Tim-3 and Lag-3, markers of T cell exhaustion. Signaling through inhibitory receptors is stimulated by respective ligands that we showed are present in the tumor microenvironment (TME). Blocking these “immune checkpoint” signals can improve T cell proliferation and anti-tumor function within various TMEs. By applying checkpoint blockade, we hypothesized that both donor and endogenous T cells will have prolonged longevity and increased effector function in our ovarian cancer model. In ongoing studies, ID8 ovarian tumor-bearing mice received MSLN-specific T cells plus antibodies that block PD-1, Tim-3 and Lag-3 checkpoints; T cell phenotype and function were characterized at early and late time-points. We will discuss our findings and the potential relevance of this combination immunotherapy as a clinical treatment of ovarian cancer.

T cell-based immunotherapy has shown immense therapeutic potential for the late-stage treatment of cancer. The synthetic ex vivo activation of T cells is a key step in manufacturing these therapies, inducing proliferation and cytotoxic functionalization of the cells before reinfusion into the patient. This is generally done with the use of artificial antigen presenting cells (aAPCs) consisting of antibodies triggering the receptor signaling necessary for activation directly conjugated to a spherical polystyrene bead. Although intended to mimic the function of antigen presenting cells (APCs) in the body, currently used aAPCs do not fully recapitulate natural size, morphology, or membrane fluidity, all of which have been demonstrated to be important determinants of activation properties. Therefore, there is a need for an activation platform that more closely mimics APCs in vivo, which could significantly improve the efficiency of T cell activation for use in cancer immunotherapies. To achieve this, we utilize cell-molded silica microparticles that retain the size and morphology of their cellular templates. The fusion of an antibody-loaded lipid bilayer to these silica microparticles results in a closer recreation of natural APCs. We have fabricated these cell-molded silica aAPCs with various cell template morphologies and lipid compositions. Using a variety of cell-based assays, we are characterizing the capacity of these aAPCs to induce T cell proliferation, cytokine release, and surface marker expression, all of which are metrics indicative of activation. If these results indicate that this platform successfully improves the efficiency of T cell activation as compared to current alternatives, this has the potential to improve the cost and scalability of these promising cancer treatments.

The research project primarily aims at better characterizing how neurons of certain types transform their inputs from “upstream” neurons into outputs to “downstream” neurons. So far in the project, it has been determined that there are major differences between Intratelencephalic (IT) and Pyramidal Tract (PT) neurons on the basis of genetics, morphology, electrophysiology and functionality. We have collected data from two genetically distinct mice. Single cell recordings reveal that PT and IT type neurons are electro physiologically different, in both the locations to which they send their signals in the nervous system and the neuron morphology. Using retrograde tracing (a research method used to trace neural connections), it was found out that PT type send their axons to spinal cord and regions outside of telencephalon region of the brain but IT were restricted to telencephalon region of the brain. Now, my primary focus will be to elucidate how the electrophysiological and morphological characteristics interact. To do this, I will use reconstructions from two photon imaged stacks of their structure imported into a simulation environment called NEURON. Using NEURON, I will try to identify the potential mechanisms that underlines the sensitivity in synaptic integration of the two neuron types. This will provide testable hypothesis for future experimentation. IT and PT type have distinct roles. IT type are sensitive to anti-depressing mechanisms whereas PT type are sensitive to ALS mechanisms. It is this property that will help us create targeted medications.

While the population in America is becoming more and more diverse, the faculty that train our future workforce are not. At predominately white institutions (PWIs) across the United States, racial disparities amongst faculty are problematic. As of 2015, African Americans made up approximately 12.7% of the United States population. At that same time, male and female African American full-time faculty at degree granting college institutions made up only 3% of the workforce. With inadequate representation of African American male faculty, there are voids in the bonding experience between a student and professor. This study critically examines the limited representation of African American men in higher education, and the effects such representation might have on students and faculty, particularly regarding mentoring opportunities. The implications of racial disparities in higher education have been explored through in-person, semi-structured interviews with African American faculty members, graduate students, and undergraduate students. The results of this project have shown that the lack of representation amongst African American male faculty is negatively impacting the college experience for not only students but also staff at PWIs. This research has gained a better understanding of the importance of mentoring and the effects of limited representation and has added to the overall conversation regarding African Americans males in higher education.

Puget Sound is renowned for its biological productivity, but seasonal upwelling feeds this system with waters rich in dissolved CO₂ and consequentially accelerates the acidification of these ecosystems. In this region, aquaculture of bivalves has important economic and cultural roles that are threatened by ongoing changes in climate and water chemistry. For mussels and oysters, shell strength and integrity are the first defense in combating biotic and abiotic stressors but exposure to low pH can drastically weaken calcium carbonate shells. This study examined the effects of variable pH on the shell strength of the Mediterranean mussel, Mytilus galloprovincialis, and the Olympia oyster, Ostrea lurida. M. galloprovincialis and O. lurida were attached to ORCA buoys at three sites in Puget Sound, at either 5m or 20m depth on the buoy tether for three months. This spatial diversity exposed the bivalves to naturally occurring variations in pH which were continuously measured in situ by the ORCA buoys. The resulting shell strength was measured using an Instron Universal Testing Machine by puncturing a small hole in each shell. These results were evaluated using a two-way ANOVA between sites and depths. We expected that both species will have much weaker shells at deeper depths where pH is generally lower. This study can provide physiological thresholds of economically and ecologically important species under current and future oceanographic conditions.

Climate change is an issue that affects every region of the world, but it has a disproportionate impact on coastal communities and developing countries. Fitting both of these criteria, Costa Rica is extremely vulnerable to the impacts of climate change. Currently, Costa Ricans are known for living “pura vida”, or the pure life, and the country consistently ranks #1 on the Happy Planet Index, a global index of sustainable wellbeing. The main goal of my study was to assess how closely a relationship with the environment impacts one’s perception of success. As an intern for Frontier Programs in Costa Rica, I engaged in conservation research in the Osa Peninsula, subsequently interviewing twenty locals to attempt to answer how environmental relationships and definitions of success are intertwined. Frontier Programs’ goal is to seek out conservation hotspots and work with locals to empower them in future conservation action. My results support the argument that a connection to the environment affects factors people use to define success: happiness, health, and job security. Costa Rica is already feeling the effects of climate change and a loss of biodiversity, and further degradation of this unique natural area has the potential to lead to a decreased connection to nature. This creates a compelling argument for enhancing the climate resiliency of Costa Rica. Closer to home, my work could be extended to make the case that Americans can increase their overall perceptions of success by developing closer relationships with the natural world. 

It is no secret environmental issues are increasing in quantity and severity with passing time. The U.S. Environmental Protection Agency (EPA) is tasked with addressing these issues through its programs and regulatory authority. With a large portion of the EPA's budget allotted to grants, it becomes increasingly important to measure the success of funded projects to ensure they are achieving their intended goals. Grants awarded for environmental education specifically bring awareness to environmental literature and curriculum. This in turn inspires critical thinking, problem solving, and action. Through my internship with the Office of Public Engagement and Environmental Education at the EPA, I aimed to discover what prescriptive criteria EPA should require from their grantees, in hopes of funding impactful projects and collecting data to leverage the program's legacy. I synthesized final reports of environmental education grants issued since 2012, interviewed EPA personnel, interviewed grantees, and conducted a thorough review of documents within the environmental education grant process. I discovered stark differences in the definitions of "success" between the grantees and their communities as compared to political and agency structures. Realigning these measurements of success allows EPA to allocate grants to promising projects and use the limited available funding to make a difference. Empowering communities through grants allows them to educate their communities in ways they know best, but also provides them with the encouragement to commit to action and use public involvement for solving environmental challenges.

Archaeologists have made efforts to increase archaeology’s accessibility to those with marginalized identities and to be accountable to communities around archaeological sites. However, alternative ways of knowing and understanding the past from non-Western perspectives remained excluded from contemporary archaeology. The impact of European epistemological hegemony in archaeology limits the frameworks and methodologies that are utilized and considered valid. As more people with marginalized identities have joined the academy, however, archaeological literature has grown to incorporate previously excluded epistemologies. The Black feminist lens only recently has been applied to archaeological theory and practice. The lens attempts to acknowledge the intersectionality of Black women’s identities as racialized and gendered people and disrupt master narratives used to demonize, control, and limit Black women. The Black feminist theoretical model relies on intersectionality and development of an empowered community, while acknowledging the difficulties Black women experience due to class, education level, etc. This paper utilizes semi-structured interviews with Black women archaeologists in the United States to gain insight into their methodologies and perspectives in the field. Additionally, this paper incorporates personal ethnographic diaries entries that are connected to my experiences as a Black undergraduate student to explore the impact of the current sociopolitical climate on my research. The broader implications of the work are towards the recognition of Black women’s intellectual production within archaeology and support the presence of Black women in the discipline as necessary interlocutors in developing liberational archaeology that uplifts voices from marginalized groups through interviews with Black women in archaeology.

Situated in the depths of a city’s music scene lies an underbelly of DIY (Do It Yourself) spaces. These spaces operate under the radar of the city’s commercial music scene found in for-profit venues, working to support experimental and small-scale artists who are often excluded from “legitimate” spaces. The DIY mentality developed from a desire to create venues that support musicians and audiences who refuse to adjust to the tastes of large music corporations. These communities host shows in spaces artists can afford, such as living rooms, basements, and warehouses. This project examines the creation and perpetuation of these underground music scenes, focusing on the development of a scene’s community and how identity is performed inside and outside of DIY spaces. This project explores how a city’s built environment (including its available housing, geographic layout, and ease of transport) impacts the way a scene functions and evolves. It teases out how these impacts are felt through observing how a scene’s social norms are performed at events in DIY spaces, examining the styles of music played within a scene, and other related factors. In order to determine how a scene's norms are specifically influenced by the spatial dynamics of a city, this paper examines the underground music scenes of Seattle and Philadelphia, a deliberate contrasting that shows how the differences and similarities in each scene can be attributed to both the cultural identity of the city as well as its unique urban environment. Whereas there are certain norms that arise out of the overarching DIY ideology (meaning they can be found in the scene of each city), there are disparate norms that are endemic to the each city’s scene. These latter norms prove a city’s built environment holds significant weight in the development of its underground scene. Ultimately, this data will provide evidence of the importance of these underground scenes within a city's arts community,advocating for their protection and support both locally and nationally. 

Influenza is a prevalent infectious disease that claims the lives of 800,000 people globally. Current diagnostic methods include cell culturing, antibody staining, and nucleic acid amplification tests that take from 4 hours to 3 days. The need for rapid, cost-effective and accurate influenza detection tests can be met by lateral flow immunoassays (LFA), which are paper-based test strips similar to pregnancy tests. Most LFAs use colored particles such as gold nanoparticles to indicate the presence or absence of a biomarker by producing a line when the biomarker is present. However, influenza LFAs require over 10 fmol of influenza nucleoproteins to produce a readable signal, which is impractical for influenza because it is present at lower levels at earlier stages of infection. There is a need for a more sensitive influenza LFA that has an improved limit of detection. Here, we investigated how replacing gold nanoparticles with quantum dots, a fluorescent label, improves assay performance when imaged with a mobile phone. We optimized our LFA by varying the concentration and volume of the reagents needed to produce a visible signal. We excited 605 nm quantum dots with a UV LED and used an iPhone SE or Nexus 5X to image the LFAs. Results showed that quantum dot-labeled LFAs imaged with cell phones had a 10x lower-limit of detection than gold nanoparticle-labeled LFAs. Limits of detection with the mobile phones of 1.5-2.6 fmol were comparable to that on a lab-based fluorescence reader, a gel imager (limit of detection of 1.9 fmol). These results suggest that cell phone imaging and fluorescent labels can be combined to make cost-effective LFAs that can be used for rapid and efficient detection in point-of-care settings.

Obstructive sleep apnea (OSA) is a condition estimated to affect 5% to 15% of the population, in which individuals stop breathing for extended periods while asleep. Treatment is usually successful when provided; however, the vast majority of OSA patients go undiagnosed, in part because the superficial symptoms of OSA in a wakeful state are varied and nonspecific, including drowsiness, hypertension, heart disease, diabetes, and depression. The current diagnostic gold standard is an overnight sleep study, which is expensive and requires access to a specialized sleep medicine facility. This motivates a need for a convenient and accurate technology to screen for sleep apnea in homes and clinics. A ubiquitous screening solution must be both sensitive to slight variations, and specific to apnea in spite of many interfering physiological factors; these challenges are further complicated by the constraints of low-cost sensing devices. Our approach is to detect persistent changes in the sympathetic nervous system that are caused by frequent apnea events; although these changes cannot be measured directly, they manifest in discernible changes to heart signals. To test our system we record cardiac and respiratory signals while participants execute a series of breathing maneuvers, such as breath holding and breath rate control. We record in parallel with (1) a smartphone running a custom application and (2) a commercially available wireless biomedical recorder. Using digital signal processing, we extract informative features from the locations and amplitudes of peaks and troughs in the PPG, SCG, and ECG signals. Equipped with these extracted features and the ground truth diagnoses provided for each patient by the Harborview Sleep Medicine Center, we use existing machine learning libraries to train a predictive model for apnea. We expect results to demonstrate a correlation between cardiac regulation and sleep apnea severity.

This research attempt proposes a novel approach to processing and utilizing aerial imagery and data for mapping. With the advancement of unmanned aerial systems (UAS), airborne data has gained considerable momentum in recent decades, revolutionizing methodologies of geographic research, law enforcement, agriculture, and mapping. Specifically, advances in consumer electronics significantly eased access to UAS and development in parallel computing has enabled machine learning on large data sets. This paper proposes an alternative method to the current practice of processing airborne data sets. Instead of obtaining aerial imagery of an object and merely presenting those objects as pixels on a map, the proposed method uses machine learning techniques to recognize the object, assign parameters to the object and render the object in a fashion that is most efficient and understandable to the end user. The object is no longer merely a set of pixels but a list of classified objects with associated parameters, an abstraction analogous to cognitive processes. This approach allows a single data set to be used in multiple fashions. For example, the data can be used to simulate changes in the environment or render the environment in different scenarios. This paper explores the methodology for collecting airborne data sets for this process and presents several cases of this using flight test data.

Music has been heavily dependent on computers since the 80’s, and with each new advancement in computers, new advancements in music soon follow. I asked myself how will the future of pattern recognition affect the music industry? This paper explores how complex pattern recognition systems, specifically artificial neural networks, might affect the next advancements in music. Melodies from hundreds of popular songs from multiple genres were analyzed by a neural network. Everything from "Tiny Dancer" by Elton John to "I’m a Barbie girl" by Aqua were used to train the network. By having the neural network produce midi tracks, I was able to import them into a professional music producing program, named Logic Pro. The neural network’s songs were then produced as if they were generated by an artist paying for studio time. The final song was uplifting, melodic and entertaining. This demonstrates the effectiveness of neural networks as a creative musical tool. The model I propose is an improvement on an existing model, an encoder to decoder neural network written in TensorFlow. Because of music’s heavy dependency on previous events LSTM(Long Short Term Memory) cells were used. To improve preprocessing I considered transposing all of the songs to the same key, C-major, this restricts the model to track less notes by limiting the scale, while still maintaining the melody of the song. I found that working with a batch of short midi loops generated by the network worked best for creative output.

Electroencephalograms (EEG’s) are a common form of measuring electrical activity in the brain. Electrical activity from the brain directly correlates to neuronal activity, providing information that can be used for disease diagnosis or research on brain mechanisms. EEG recordings are limited in practicality and efficiency in some circumstances due to poor spatial resolution, vulnerability to noise, and consistency. Subdermal electrodes are unable to capture deep brain activity, which can only be obtained through surgically implanted intracranial electrodes. As a result, for patients in a condition where surgery is not optimal, the subdermal EEG offers little to no information in terms of deep brain activity. Through previous work, we have shown that applying 1050 Hz pulsed focused ultrasound (pFU) resulted in EEG readings above normal physiological frequencies. Natural brain activity frequencies can be derived from the amplitude demodulation of the 1050 Hz signal. The ultrasound is amplifying the electrical activity in the region it is focused upon, allowing the EEG to record these signals. In this study, we attempted to increase the capabilities and specificity of EEG noninvasively through coupling it with pFU. We continued our previous work by applying pFU transcranially to the left visual cortex of a C57BL/6J mouse brain while stimulating the right eye with light. The observed frequencies collected by EEG were analyzed for neuronal stimulation in addition to sensory stimulation elicited from the ultrasound. A technological breakthrough in this field may someday lead to the ability to measure brain activity non-invasively from anywhere in the brain.

Garbage collection is a method of performing automatic memory management which generally leads to less complex and more maintainable source code, but it has a cost of performance hits and pause times. The D programming language is a newer high-level general-purpose programming language which relies on a garbage collector for several language features, though it consistently receives criticism for this decision due to perceived loss in performance. To increase the efficiency of D's garbage collection procedures, two ideas are explored: using an alternate layout for objects in memory and eliminating the requirement for pause times under certain conditions. The first prototype explores storing objects in memory based on type and not by size, allowing the system to take advantage of type information while caching it at the same time. The second prototype takes this idea and then explores implementing a collection cycle in such a way as to run concurrently with the user program so long as the machine can continue to fulfill allocations. Both prototypes are compared against D’s existing garbage collector using benchmarking tests provided by the language maintainers. These comparisons examine memory usage, allocation time, pause time, scan time, sweep time, and total running time, using an AMD R5 1600X 3.6 GHz and Intel core i7-6800 3.4GHz on Ubuntu 16.04, and an AMD R51600X 6-core 3.6 GHz and Intel i7-4790 4-core 3.6GHz on Windows 10. The findings will show if alternate memory layout allows for new optimizations for allocations and collection techniques and if preventing a total stop-the-world period is worth the overhead costs of synchronizing the garbage collector and program threads.

Our work is an attempt to revolutionize the building industry by rethinking concrete formwork by eliminating dimensional timber formwork and replacing it with a combination of the existing PERI modular formwork system, fabric, and various constructed inserts. Not only would the customizable secondary systems we have studied are cheap to construct either on site or in a factory alongside PERI modular parts, but they would also be reusable, perhaps indefinitely. In the long run this system could minimize cost on a single job site as well as overall - as the formwork is reusable, highly mobile, flexible, and quick to install. Our system also introduces controlled organic forms, often avoided in concrete due to the difficulty of shaping rigid formwork. By using fabric, complex curvatures can be achieved that are created wholly by setting parameters (fabric excess, insert pieces, etc.) And letting the forces of hydrostatic pressure naturally dictate the ultimate form and aesthetic.

Pregnant women often get their bellies touched without their permission by people ranging from family members, to coworkers, to strangers. While usually well-intentioned, people who touch pregnant bellies are unaware that their actions may be unwanted and invasive. Previous works, such as Asta Roseway’s Printing Dress, have shown that wearable computing can bring attention to social issues by provoking discourse. Those works lead us to our wearable design that highlights the issue of personal space for pregnant women. We implemented a maternity shirt that reacts to inappropriate touches upon contact in various ways, such as displaying messages, vibrating, and setting off an alarm. We plan to deploy this shirt on experimental participants and gather qualitative data in addition to the quantitative data collected through the shirt about when and where touches occur. Moreover, findings from the experiment will provide insight into pregnant women’s experiences, and how to design wearables that benefit to pregnant women. Our future goal is to have the shirt deter the toucher as they approach the belly. Through this interactive design piece we hope to raise awareness and provoke conversation around themes of consent, inappropriate touching, and women's bodies.

Food waste is a pressing global issue. In the U.S. alone, 40 percent of food is wasted. With a 15 percent reduction, we can help feed more than 25 million Americans yearly and provide meals to the 15 percent of U.S. households who are food insecure (USDA). The University of Washington (UW) is taking strides to address this issue by working with food recovery agencies. However, these agencies are overworked and their food recovery program requirements deter some dining halls from participating. Utilizing a user-centered-design approach, our team researched, designed, and built an open source website to facilitate food recovery. Over the last 6 months, we employed six research methods: (1) we conducted a competitive analysis of food recovery systems; (2) we interviewed managers at UW dining halls and food service offices, 50 local shelters, and 6 food banks; (3) we completed a contextual inquiry of current food delivery practices; (4) we incorporated participatory design practices with 4 dining hall managers, 3 shelter managers, and 16 students; (5) we conducted iterative in-person usability tests with 25 participants including shelter and dining hall managers, and student groups; and (6) we deployed an online survey to understand the motivation and behavior of student volunteerism, receiving 78 responses. Among our many findings, we identified the need for improved communication among agencies, consistent and universal donation records, and strategies for utilizing student volunteers for donation deliveries. Currently, we are live-testing our website with one UW dining hall, two shelters, and two student volunteer groups. Our interactive, responsive open source website should prove scalable for global adaptation. Universities and corporations worldwide can utilize this system to improve their own food recovery efforts. Through our work, we are educating the public on the food waste epidemic, while building a network that prompts communal action.

The development of neurodegenerative diseases, such as Parkinson’s, Huntington’s, and Alzheimer’s affect millions of people every year. Previous studies have shown that an enzyme found in the endemic Herpes Simplex Virus (HSV-1); UL12.5, degrades the mitochondrial genome, which we hypothesize may predispose patients to neurodegenerative conditions. A majority of the human population is infected with HSV-1 and other herpesviridae, which encode similar enzymes, and their reactivation is commonly seen throughout life. We have found that the degradation of mitochondrial DNA by UL12.5 activity is widely conserved and when UL12.5 is expressed in the model organism, Caenorhabditis elegans (C.elegans), mitochondrial DNA content drops nearly 10-fold. Interestingly, we find that activation of the HSV-1 UL12.5 enzyme alters cellular proteostasis; the cell’s mechanism for maintaining properly folded and functional proteins. This change in proteostasis alters the aggregation of misfolded proteins, especially those involved in the cause of neurodegenerative diseases, and leads to neurological phenotypes like paralysis, which we can quantify in the worm. To study the enzymatic activity of the UL12.5, we used modified worms expressing the protein using an inducible transgene that can be verified by fluorescent microscopy. The effects of the UL12.5 activity is determined by tracking lifespan of worms, performing paralysis assays, and counting protein aggregates with controls that use a catalytically inactive version of UL12.5. We have also found that Emodin, a compound found in traditional Chinese medicine, which has previously been shown to inhibit UL12.5, alters the activity of UL12.5 in a worm model of Huntington’s disease. We hypothesize that activation of this enzyme may cause similar pathologies in the human brain and may be a causative factor in human neurodegenerative disease. Further, inhibitors of UL12.5 like Emodin may prove useful therapeutics for treating neurodegenerative diseases.

Black women are known to wear their hair in different ways from braids and locs to weaves and wigs. Black hair is a way of expression and a lot of thought goes into the process and maintenance of black hair. Early African civilizations used hair as a signifier for their wealth, rank, religion, and marital status and the Afro hair was seen as a political symbol for black power and self-love. Hair is so important to black women that a 2016 Perception Institute research found that black women reported spending more on their hair and booking more professional hair appointments than white women. And while our hair means so much to us, it remains a mystery to many non-black people and so we become the objects of inquiry: we are constantly fielding questions about our hair. I examined the ways in which questions like: “can I touch your hair?”; “how often do you wash your hair?”; and “is your hair real?”, affected black women’s self-esteem and confidence. The study first established what was an intrusive question and the historical and political implications of black hair. Through a focus group with 10-15 black women ages 18-24 along with follow-up interviews with some of them, the study highlighted some of the experiences young black women have faced about their hair and the impact of the intrusive questions on how they viewed themselves. I expected the focus group to reveal that those intrusive questions left black women feeling uncomfortable, inauthentic or fake, and stopped them from frequently changing their hairstyles.

Mitosis is a process important for the regulated division of cells. In cancer cells mitosis is often dysregulated, which can cause cells to split uncontrollably. One important protein that plays a key role during mitosis is the protein kinase Polo-like Kinase 1 (plk1). The function of Plk1 is to regulate centrosome maturation, bipolar spindle assembly, and mitotic entry, making it a very important protein throughout mitosis. To understand how it functions during mitosis we can use drugs that turn off the activity of Plk1 to mimic what occurs when the protein is malfunctioning. Drugs like BI2536, a small-molecule inhibitor that turns off Plk1 activity in mitotic cells, have provided insight into how Plk1 functions; however, these drugs are not selective enough to inhibit protein activity at distinct locations in the cell. To address this problem, we use a technique called SNAP-tag to localize BI2536 to specific organelles within cells. Using genetic engineering approaches like cloning, virus generation and stable cell production, I helped make cells that express a SNAP protein linked to a PACT domain. PACT localizes to the centrosomes in dividing cells and allows us to bring SNAP protein only to that location. Our modified drug enters cells, binds to SNAP-PACT, and selectively inhibits Plk1 activity at the centrosome of cells. Through experiments I have run, we have shown that we are able to inhibit Plk1 activity in vitro and in vivo. Using immunofluorescences and super-resolution microscopy, I have shown that local targeting of CLP-BI2536 to the centrosomes causes a greater reduction in active Plk1 (p-plk1) than traditional global drug delivery. In the future, I hope to use this approach to investigate the activity of another mitotic protein, Aurora A, in order to further explore the role of mitotic kinases during the cell cycle. 

There has been a research effort in exploring RFID (Radio-frequency identification) interfaces. RFID is a form of wireless communication that uses electromagnetic coupling in the radio frequencies to uniquely identify an object, person or animal. By expanding on previous work in paper and RFID technologies, we are able to create new interactive capabilities from paper and RFID. During my time with the Ubiquitous Computing Lab, my goal is to find a technique using capacitive sensing, conductive ink, and RFID tags in order to create an interactive touch surface. An RFID antenna can read an RFID tag and give information pertaining to that tag, for example, tag ID, time, a tag’s doppler shift, tag’s signal strength and more. My research has been exploring the relationship among these variables and creating a quantitative model that can map for continuous interactions. With such a model, one can make that surface customizable for a variety of interactions. 2D Sense strives to enable 2-dimensional touch interactions on paper by applying signal processing techniques towards existing RFID technology.

River ecosystems depend on services salmon populations provide. Coho salmon, Oncorhyncus kisutch, supply valuable nutrients for mammals and birds and offer economic benefits for the Pacific Northwest. Salmon rely on water quality in freshwater streams during successful seasonal spawning. However, for over the past 15 years, research determined that urban stormwater results in the mortality of Coho salmon. Exposure to urban stormwater is toxic to Coho salmon, killing them in hours. This phenomenon is known as pre-spawn mortality (PSM), and it kills salmon before they reproduce. If this phenomenon continues, Coho salmon could go extinct. Previous studies have linked highway runoff and pre-spawn mortality. However, they indicate that basic water quality parameters such as temperature and pH and “typical” stormwater toxicants such as metals and pesticides are not the cause of PSM. Current hypotheses point to an unknown organic contaminant that is linked to urbanization and is probably present from roadways or cars. Previous studies have also shown that bioinfiltration of stormwater through a mixture of sand and compost can protect Coho salmon. The goal of this study was to investigate removal of organic contaminants in a pilot-scale compost-amended bioswale (CABS). The pilot-scale CABS was based on a field-scale bioswale that is operated by WA DOT and located on SR-518. In this study, we developed methods to extract water with suspended sediment (whole water), as well as extract filtered water and total suspended sediment (TSS) separately. Whole water and filtered water were extracted by solid phase extraction (SPE), using Infinity® SPE cartridges. TSS was measured using EPA Method 160.2, and captured solids were extracted with methanol. Extracts were then analyzed by liquid chromatography-high resolution mass spectrometry. These methods were then applied to evaluate removal of organic contaminants in the bioswale, including performance at multiple hydraulic retention times.

The purpose of this research is to find data patterns of DC motor failure through radio frequency emission. To collect data for classification, three sets of five DC motors were modified to exhibit three common motor fault issues: armature winding resistance variation, brush contact/air gap, and bearing friction. A set of control data from unmodified motors was also collected. The motors were run for a set period of time at the manufacturer recommended voltage and rpm band with no load. The data was collected via a RF receiver and processed digitally. Using a Python-based program, known-good and known-bad data was run through a machine learning program. The program was then tested for accuracy and precision of diagnosis using a wider spectrum of faulted motors, including variation of fault, load, and size of motor. The hypothesis of this research is that radio frequency emissions generated from a defective DC motor show detectable differences from a normally functioning motor, the differences of which may show signature patterns that can be isolated using classification  through machine learning programming and used to predict onset of failure.

The vestibular system is integral to reflex behaviors that allow humans to walk and see clearly. For example, the angular vestibulo-ocular reflex (aVOR) stabilizes images on the retina by using input from the semicircular canals to produce fully compensatory rotation of the eye. When these systems fail, patients are disabled. Understanding the vestibular system can help us create effective treatments for vestibular disorders. Our lab is developing a vestibular neural prosthesis based on such knowledge. In this proposal, we are studying large gaze shifts accomplished with eye and head movements. The eyes saccade to a target as the head starts to rotate. During this combined movement, ratio between head velocity and compensatory eye counter rotation (VOR gain) is continually adjusted to accomplish an accurate gaze shift. When the eyes move toward the target, the VOR may be reduced or eliminated. When the eyes reach the target, the gain returns to 1.0 to stabilize the eye on the target. Our study utilizes head free Rhesus monkeys to assess the gain of the VOR before, during, and after a gaze shift. The monkeys are trained to follow a laser target, allowing researchers to induce gaze shifts by changing the laser position. We utilize only horizontal shifts, and only stimulate the horizontal canal. We record change in eye velocity in response to implant stimulation at different trial times. We hypothesize that the gain of the VOR is decreased when the eyes and head are moving toward the target. By stimulating before, during, and after and evaluating the change in eye velocity, we can infer the magnitude of change induced by vestibular input and the instantaneous gain of the VOR. The results of this study will provide insight into how the brain utilizes vestibular information during combined head and eye movements.

Just as mountain-building from the convergence of tectonic plates changes weather patterns, the opposite, monsoons in southwest Asia, may have also influenced the erosion of the Himalayas. Turbidite sediments collected in International Ocean Discovery Program cores from the Bay of Bengal contain material eroded from the Himalaya, which may have been shaken up during monsoon destruction then resettled. Magnetic particles extracted from those turbidites were tested for magnetic properties and identified using scanning electron microscopy. Magnetic minerals positively identified include magnetite and sulfides. Linking these minerals to their sources in rocks and soils from the Indian Subcontinent and the Tibetan Plateau, we will be better able to model the erosion patterns back from 14,000 years ago, potentially correlating heavy storm activity in one region to massive sediment deposition downstream. This data may suggest whether the erosion from weather over a long period of time creates a negative feedback loop causing more intense climates overall. Further data that refines the ages of sediment layers can also relate how the severity of storms affects the increase in mountain erosion and runoff.

During the Space Race, NASA calculated lunar rocket trajectories by using Euler’s Method to estimate the differential equation obtained by numerically integrating Newton’s Laws of Motion. At the time, computing power was scarce, costly, and primitive. The objective of this project is to develop an interactive MATLAB application that leverages modern computing architecture to accurately and efficiently approximate lunar rocket trajectories based on multiple variables relating to a rocket's journey to the Moon using the Runge-Kutta method. The Runge-Kutta method is a more accurate and sophisticated version of Euler’s method as it uses a multi-stage algorithm that involves slope calculations at discrete time values. This project will bring valuable input to the feasibility of using such numerical methods in approximating lunar trajectories to the industry. The rocket emulated in the program will be based on NASA's Saturn V rocket. Our application will simulate three phases of travel to the moon: achieving Earth orbit, lunar transfer orbit, and lunar orbit. It will consider variables such as time, distance, velocity, acceleration, position, rocket thrust, exhaust velocity, mass flow rate, and aerodynamic drag. The application will allow users to adjust various parameters in real time and see results graphically.

The behaviors of female mosquitoes related to disease transmissions such as host-seeking and egg laying are heavily studied. It is also known that both male and female mosquitoes acquire sugar from plants. However, mosquito-plant interactions are relatively understudied even though both male and female mosquitoes rely on plants for sugar. This mosquito-plant interaction allows for mosquitoes to act as potential pollinators. Some researchers have argued that mosquitoes are generally nectar robbers, while other studies have shown mosquitoes can indeed contribute to pollination. However, their significance as pollinators has not been explored. Here, we discuss a species of snowmelt mosquito, Ochlerotatus communis, a major pollinator of Platanthera obtusata, the blunt-leaved rein orchid. Orchids utilize pollinia, or pollen sacs, which attach to stereotyped locations on their pollinators. This consistency ensures successful pollination on subsequent visits. In order to maintain this consistency, the morphology of mosquitoes should match that of the flower for successful pollination leading to higher reproductive success for the plant. Through multivariate linear measurements of mosquito head characteristics, we found that the proboscis length was a distinguishing character that accounts for the morphological variation among different species of mosquitoes that are sympatric with the P. obtusata. Our finding indicates that there is a possible morphological match and suggests that there is a possible match with the nectary length of the orchid and morphological characters of the mosquito. Our study demonstrates the first-ever analysis of mosquito morphology within the context of pollination. To further test this, additional studies can be done on verifying the significance of the lengths of the proboscis and nectary for successful pollinia removal.

At the terminus of every robotic arm is an end-effector. These are the hand-like devices that directly interact with the environment. Collecting data from the vantage point of an end-effector is highly desirable, though difficult to accomplish in practice. Wired data transmission solutions which use internal cables suffer from signal degradation due to proximity to power conduits. Moreover, the solutions which use external cables are subject to tangling and often impose limits on the robot’s kinematics. Finally, existing wireless data transmission solutions are rarely used due to the low transmission rate, high latency time and unstable connection. This research focuses on developing a general approach to stream visual (RGBD) and haptic (force) data wirelessly to other devices. The resulting system should consist of an architecture which interfaces with a suite of end-effector sensors and handles signal compression, transmission, and decompression efficiently. Additionally, this project involves a hardware design portion which aims to neatly package and mount this infrastructure at the robot end-effector while satisfying power and kinematic constraints for the robot. This research chose the Intel Joule, an embedded Linux board, as the infrastructure to handle wireless transmission. The embedded board uses a low-level Python networking package, which forms the connection to transmit data to other devices on the same network. This project implements packages to encode, transmit and decode the data stream with Python. The receiving device decodes the compressed data and makes the data available to other devices on the same network. This project allows sensors and the main computer of the robot wireless connected and future robot would operate movement more freely.

Predators exhibit top-down effects on plant communities by altering the abundance and behavior of their herbivore prey. Disturbance regimes such as wildfire may impact the strength and nature of these interactions and their corresponding effects on plant communities. In 2015, wildfires burned through areas in northeastern Washington impacted by the recolonization of gray wolves (Canis lupus) and inhabited by their two main prey species, mule deer (Odocileus hemionus) and white-tailed deer (O. virginianus). We are using data collected in burned and unburned areas across wolf-impacted and wolf-free sites to explore the relationship between recent wildfires and the effects of predators on plants. Data on plant species presence, percent cover, and browsing extent within each plot and associated controls will provide an index of browsing intensity and plant species selection by deer. Our preliminary analysis contrasts plant percent cover as a function of fire, wolf-presence, and measured landscape variables. Our findings will yield a better understanding of the top down effects of predators like wolves in areas like the American West that are predicted to be increasingly affected by wildfire.

The ARGO float program consists of over 3,000 profiling floats that are free drifting and take temperature and salinity measurements of the upper 2000 meters of the ocean. Understanding why these floats are failing prematurely in the field is important to ensure the longevity of floats in the future and the overall effectiveness of the ARGO array. In this investigation I looked primarily at floats deployed by the University of Washington since 2005 to determine the success rate and identify problems in the floats deployed by our lab. This was accomplished using engineering data communicated back from the floats which includes the piston position, which is used to control the density of the float, battery levels, pressure sensor readings, as well as temperature and salinity readings. Each float also has an associated energy budget model which was used to calculate the number of expected profiles based on the batteries powering the float. Preliminary results have uncovered a significant number of floats having a gain in buoyancy, followed by a sudden and catastrophic buoyancy loss, and soon afterwards, float failure. Based on what we observed on a shoaled float with corrosion around the endcaps, we believe this loss in buoyancy is due to corrosion. A float which showed similar buoyancy trends was recovered and also had significant corrosion around the endcaps, confirming that we are able to identify corrosion using engineering data. Energy budget models have identified that most floats will achieve approximately 80% of their expected lifespan, which is considered a successful float lifecycle. Having reliable methods to identify failure modes using only engineering data will enable us to remotely diagnose problems with a deployed float and correct those issues for floats we deploy in the future, extending the life expectancies of floats in the future.

Changing developmental patterns is an essential strategy for plants to survive environmental stressors, and the hormone auxin coordinates much of plant development. In the auxin signaling pathway, Aux/IAAs are co-repressors that block expression of auxin target genes. When auxin is present, Aux/IAAs are ubiquinated by an E3 ligase and then degraded via the proteasome. This results in an increase of auxin response gene expression. Past research in the Nemhauser lab found that a dominant mutant in the Aux/IAA known as IAA28 alters the placement of lateral organs around the stem (a process called phyllotaxy). IAA28 loss-of-function mutants show no phenotype, so we hypothesized that another gene or genes could be acting in a redundant manner. IAA28 is closely related to two other Aux/IAAs called IAA18 and IAA26. Using CRISPR/Cas9 technology, I am making triple mutants that lack function of IAA18, IAA26, and IAA28. Once I have these mutants, I will measure phyllotaxy and other developmental phenotypes to look for differences when compared to wild-type plants.

In 2015, the WHO reported 27.4 deaths for every 100,000 people per year in Uganda were attributable to road crashes. Road crashes are one of the top ten causes of premature death in this East African nation of about 41 million people. While youth and young men are at the highest risk, the ripple effect of even a single death includes costs of treatment, lost wages, and compromised health of a whole family. We used roadside observational methods to measure the frequency of phone use while driving. In a roadside spot survey of Ugandans, we also asked about attitudes, knowledge, beliefs, and personal usage of cellphones while driving.While it is illegal in Uganda to talk on the phone while driving, drivers' frequency of phone use was comparable to rates seen in the U.S. In our survey, those who admitted to using their phone were more likely to be educated on the law and believe their behavior was dangerous compared to those who did not use their phones while driving. One explanation for this finding is that businesses are requiring employees to use their phones while driving, and those with these jobs could be more aware of the law in order to conceal their behavior. The Ministry of Health, police, business, and many other transportation related departments all have a policy role in reducing distracted driving. Action from these groups has been shown to influence and reduce risk behavior.

The Digital Future Lab is creating a 3D strategy game called “SEED”. It is a reverse tower defense game in the sense that rather than set up obstacles (towers) on a playing field to stop or destroy waves of enemies from reaching their destination, you set up towers, in this case helpful characters called Muses, to help waves of creatures called Tali along their hazardous journey across the playing field. My responsibilities for SEED were making assets and creating concept art to help in the 3D pipeline. Using Adobe Photoshop, I painted concept art that refines the 2D designs of other students to prepare them for modeling and texturing in a 3D space. It is difficult to imagine certain design or visual ideas without a visual representation and so I created diagrams and sketches to aid my team members. In order for a character to work in a 3D space, certain aspects of its design needed to be altered in order for it to be easily animated, as well as for it to look good in the game itself. In addition to designing these characters, I modeled them using Autodesk Maya and textured them using Substance Painter. As of now, these characters have been fully modeled and are in the game. Apart from that, I also determined the look and feel of the environment of the game and created concept art in order to unify the visual experience between all these different, complex elements. Ideally, all this work will go towards immersing and wowing a player when they first load into the game.

The field of robotics attempts to replicate human intelligence by harnessing vast amounts of information, and will heavily influence next generation technologies. Of course, in order to operate in an intelligent manner, our robots must be equipped with sensors that can provide informative data. By endowing our robots which such sensors, we can enable them to assist humans that are dependent on others for completing every day tasks, such as opening doors, picking up fallen objects, and pulling wheelchairs. Up until recently, many robots required their sensors to be wired to their main computers, potentially impeding their movement and/or limiting the types of sensors that they can employ. Our work, in particular, focuses on pre-touch sensors, which are sensors mounted to the robot's fingers that allow it to sense an object prior to making contact. This project redeveloped the pre-touch sensing system such that data from up to five sensors is wirelessly transferred to the robot's main computer. There are five micro USB ports connecting to the five fingertip sensors, all of which are controlled by the main USB hub. Vocore, a single-board computer, is incorporated, and this Linux based mini-computer is an essential component for sending the sensor data via Wi-Fi to any selected computer. Additionally, the elimination of wires makes it much easier to reconfigure the form factor of the pre-touch sensing system. As a result, these versatile sensors could be applied to any robot in the world.

Digital mapping and routing has completely changed the way people interact with maps. However, a large percent of the population is, in general, not served well by most current popular digital mapping services due to two primary reasons. First, most maps do not focus services for pedestrian access. Second, unlike other areas of digital information delivery, mapping and routing has not gone through customization and personalization strategies to improve people's experience of and access to digital maps. There are many such human factors, ability characteristics, cognitive or emotional parameters, that are difficult for users to articulate numerically, but significantly impact the way in which urban environments are experienced and enjoyed by pedestrians, or the manner in which digital mapping information can be accessed. AccessMap is a map for those with disabilities, providing routes and information to wheelchair users, cane users, and others who may have difficulties getting around. Currently, users don't have too much freedom to control their preferences when they use AccessMap and they didn't have a profile to save the preferences they chose. Therefore, we tried to understand users' needs and modified existing interfaces to include more features. In our research, we are trying to design a better interface to address the diverse spectrum of user needs in a comprehensive and human-understandable way, as well as provide a platform to save and refine those preferences. We focus more on the user experience side of this project, we run varied research including scholar research and survey. We consolidated findings into personas and ideated scenarios and user flows to guide our design and envision how users would interact with the product. Our future goal is to run more usability tests with potential users for the purpose of improving application’s user experiences and evaluation our design.

Rhabdomyosarcoma (RMS) is a devastating pediatric soft tissue sarcoma. The major RMS subtype, embryonal RMS (ERMS), is often driven by abnormal RAS activity. Activating mutations in the NRAS oncogene, for example, drive cell growth in many types of cancer, including RMS. Unfortunately, there are currently no drugs that can block NRAS activity. Recently developed CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 gene editing technology has become a powerful tool to disrupt gene function in a wide range of organisms and cell types. My research investigates the therapeutic potential of using CRISPR/Cas9 gene editing in RMS to target a cancer-causing mutation in the NRAS oncogene. To target the mutation in NRAS, I used a Gibson molecular cloning strategy to create a DNA construct expressing the SaCas9 coding sequence DNA and two CRISPR gRNAs. One of the gRNAs precisely matches the activating A183T NRAS mutation found in some ERMS tumors. Lentiviruses were produced from these constructs to deliver the gene editing NRAS A183T therapy to ERMS cancer cells. The efficiency for targeted disruption of the NRAS mutation by the CRISPR/Cas9 technology has been confirmed as comparable to general targeting of NRAS, and the mutations produced by this therapy have been profiled through next-generation sequencing to analyze targeting specificity in normal cells. If this therapy is effective in inhibiting RMS tumor growth, this mutation-specific CRISPR/Cas9 targeting strategy can be further developed into a treatment for cancer caused by this mutation. In contrast to conventional chemotherapy treatment, which kills both normal and cancer cells, this CRISPR/Cas9 gene editing therapy could be introduced with the aid of a suitable delivery system into the cancer cells of a patient carrying the NRAS A183T mutation. The treatment would then target and selectively kill NRAS mutant cancer cells, thereby achieving therapeutic results without causing significant side effects.

During development, profound changes occur in the liver from a hematopoietic organ to a major organ for xenobiotic biotransformation. Developmental regulation of epigenetic modifiers, such as factors involved in DNA methylation and histone modifications, may modify the transcriptional output of drug-metabolizing enzymes. The goal of this study was to develop an in vitro model to recapitulate human liver development using HepaRG cells and implement this model in investigating the developmental regulation of epigenetic modifiers and drug-metabolizing enzymes. Previously, HepaRG cells were maintained in proliferative phase and were tested up to 14 days at fully differentiated stage. In this study, we collected cells during differentiation from 0 to 14 days, and isolated total RNA for RT-qPCR of epigenetic modifiers and drug-metabolizing enzymes. Among a panel of 92 epigenetic genes, there were 52 genes differentially regulated at earlier time points as compared to the fully differentiated stage. Most of these epigenetic modifiers increased during differentiation and reached a plateau either at Day 7 or Day 14; whereas the class II major histocompatibility complex transactivator (CIITA), which has an acetyltransferase domain, gradually decreased during differentiation. The adult hepatocyte marker albumin gradually increased and reached a peak at Day 7, which decreased thereafter. The mRNA of the fetal-specific drug-metabolizing enzyme cytochrome P450 3A7 (CYP3A7) was high between Day 2 and Day 3 but decreased rapidly thereafter. Conversely, CYPA3A4 mRNA was increased till Day 7, when peak mRNA levels were observed, and decreased thereafter. In conclusion, the present study is a first step in establishing a working model to investigate human liver development in vitro.

Soil contamination occurs when human-made chemicals seep into the ground. It can have negative effects on human and animal health, pollute groundwater, and reduce crop yields. Chlorinated ethenes are toxic chemicals used in degreasing and dry cleaning, and their improper disposal can result in contamination. Before remediation to remove the contaminant happens, the affected site must be assessed. Magnetic susceptibility is a measurement of a substance’s ability to be magnetized when put in a magnetic field. Magnetite, a common mineral with the formula Fe₃O₄, is strongly magnetic and has a high average susceptibility. Indeed, magnetite can dominate the magnetic properties of Earth materials such that magnetic susceptibility can be used as a proxy for magnetite abundance. Soil contaminated with chlorinated ethenes has several biotic and abiotic degradation pathways. One abiotic pathway is through magnetite, which is known to affect the detoxification of this pollutant. Choosing the best pathway is aided by the software tool BioPIC. In this study, soil was analyzed using a protocol developed for frequency-dependent discrete specimen magnetic susceptibility measurements to determine magnetite content, and thus to estimate ethene degradation rates. Frequency-dependent measurements allow for estimating magnetite particle size, which influences reactivity. We also explore other magnetic properties to more conclusively determine magnetite concentration. A further avenue for research in the future would be to discern the source of magnetite in the soil, whether it is transported by water or air, precipitated from chemical solutions, or synthesized by certain bacteria. Abiotic degradation of ethenes is just one parameter to consider in an overall remediation strategy. Options for remediation include removing and disposing of the affected soil, containing the soil in place, aerating the soil, and using microorganisms to digest the pollutant.

Studies have shown disparities in environmental justice as manifest by the variation of air pollution exposure based on race and socioeconomic status (SES) on a national scale. This study focused on determining whether a similar association exists in Washington. I hypothesized that in areas where people of color are the majority residents, exposure to air pollution as measured in PM2.5, will be higher. I also hypothesized that there would be a higher average concentration of PM2.5 in low-income areas. PM2.5 are solid particles with a diameter smaller than 2.5 micrometers. In this cross-sectional study, I used linear regression and analysis of variance to evaluate my hypotheses where I treated income as a continuous variable and majority residency by race as a categorical variable. Overall, I found a negative association between PM2.5 and income, which supports the hypothesis. I estimated that PM2.5 is expected to decrease by 0.03 µg/m3 on average per 10,000 dollars increase in income [95% CI: -0.032, -0.02.8]. I controlled for urbanity and education. When I considered effect modification, I found that the negative association was not present in rural areas. In descriptive analyses, I considered four different racial categories (White, Black, Latinos, and Asian). I observed that for areas where black people are the majority, the PM2.5 exposure is the highest, with a mean of 6.86 µg/m3 [95% CI: 6.82, 6.87], with a maximum of 7.65 µg/m3 and a minimum of 6.06 µg/m3. In comparison, in areas where white people are the majority population, the mean was 6.12 µg/m3 [95% CI: 6.11, 6.13], with a maximum of 8.12 µg/m3 and a minimum of 3.54 µg/m3. I conclude that there is a disparity in air quality based on ethnicity and SES in Washington State. Directly or indirectly, environmental injustice contributes a greater risk of health issues and diseases.

Rhabdomyosarcoma (RMS) is an aggressive malignant pediatric cancer characterized by pathological skeletal muscle development. Due to a small accumulation of genetic mutations, RMS tumor progression is believed to be driven by epigenetic regulators, which modify chromatin structures to control gene expression. Through gene expression and knockout experiments, our lab identified components of the Switch/Sucrose non-fermentable (SWI/SNF) complex as being potentially involved in RMS growth. SWI/SNF is a family of chromatin remodeling complexes that may function in histone binding and chromatin organization to regulate gene expression. To identify any possible interactions and understand the role SWI/SNF genes in RMS, we developed a large-scale multiplex CRISPR/Cas9 genetic screening system that targets 50 epigenetic regulators, including all the SWI/SNF components. These genes are targeted individually and in every possible two-gene combination. CRISPR, a gene editing technology which uses guide RNA (gRNA) sequences to direct double-stranded cuts in DNA, allows us to knock out genes in cells to gain insight into their function. I have made the CRISPR targeting DNA constructs for the SWI/SNF genes to be included in the library of epigenetic regulators for the genetic screen. We are currently introducing the CRISPR library into human RMS cells to assess the effects of all possible combinations of single-gene and dual gene-knockouts on tumor cell growth. Using this large-scale multiplex genetic interaction screen, we hope to identify genes and gene combinations that are essential to the growth of RMS cells. If two genes have cooperative or redundant function in promoting RMS tumor growth, a dual-gene knockout is expected to result in a more significant reduction in cell growth compared to targeted disruption of either gene alone. The study will provide valuable insight into genetic interactions among key epigenetic regulators in RMS and potentially identify novel therapeutic targets for the treatment of RMS.

The microbial community residing in the gastrointestinal tract, called the gut microbiota, plays an important role in host energy homeostasis. Since energy homeostasis is essential for survival, it is plausible that neural circuits involved in maintaining host energy homeostasis would evolve to shape the composition of the gut microbiota in alignment with the energy needs of the host. In humans and mice, neurons in the arcuate nucleus of the hypothalamus that express agouti-related protein (AgRP neurons) play an important role in stimulating food intake and maintaining energy balance. AgRP neurons are maximally active during starvation conditions; thus, we are investigating whether they help conserve energy under these conditions by altering the composition of the gut microbiota to a state with a greater capacity for energy harvest. To test this hypothesis, we expressed an excitatory designer receptor, the hM3Dq receptor, in the AgRP neurons of mice and then analyzed the bacterial composition and energy harvest capacity of the gut microbiota of these mice following pharmacological activation of the hM3Dq receptor relative to unstimulated control mice. We assessed the bacterial composition of the gut microbiota using 16S rRNA amplification, sequencing, and characterization, and we assessed the energy harvest capacity of the gut microbiota by determining the energy content of the mouse fecal matter using bomb calorimetry. Our results show how AgRP neuronal activity influences the composition and energy harvest capacity of the gut microbiota. These results reveal that the central nervous system can shape the gut microbiota to promote energy balance. This finding contributes to a better understanding of why and how gut microbiota changes occur, which may be relevant to understanding metabolic diseases such as obesity.

 Despite 97% of climate scientists agreeing that the current rate of climate change is human-caused, within the United States there is vast disagreement over the causes of climate change, as well as how the US should respond to this threat. These differences fall largely along party lines, with Republican party elites arguing that climate change is not a human concern, whereas Democratic elites tend to fall in line with climate scientists. As climate change continues to threaten physical safety, economic security, and food security, will people change their party affiliation? The purpose of my research is to discover how and where physical climate change is perceived as a threat, and whether it is strong enough to influence one’s political decision making. Huge partisanship realignments are rare but have occurred in the past when a large group of people feels that their current political party isn’t taking steps to confront the fears of the party base. For my project, I have compiled research on what influences political beliefs and motivates realignments, as well as the impacts of climate change in each region of the United States in order to assess where and what the threats will be. This research illustrates how people react and how they use their social power to protect themselves in light of a perceived threat in the form of a map projection for how partisanship may look like in the wake of climate change in 2100. It also shows in what ways climate change is “proven,” and what changes are viewed as most socially threatening.

Hosted through the Earth and Space Sciences department, HuskySat-1 is a 3U (30cm x 10cm x 10cm) satellite manifested for launch into low earth orbit in late 2018 or early 2019. HuskySat-1 is primarily an undergraduate research effort, but includes graduate students and industry partnerships. It spans many departments including Earth and Space Sciences, Electrical Engineering, Mechanical Engineering, Aerospace Engineering, Physics, Mathematics, and many others. The mission goals are to establish a space presence for the University of Washington, and to test novel hardware fabricated here at the University of Washington. Of particular interest are the Pulsed Plasma Thruster (PPT), a plasma propulsion device designed and fabricated entirely at the University of Washington in the Advanced Propulsion Labratory, and the K-band communication system, a high-frequency, high-gain antenna capable of transmitting data at megabits per second from orbit to Earth. The satellite also includes several other subsystems including power, attitude control, structures, computers and data handling, and low-gain communication. The mission strives to provide experience in real-life engineering to the entire team, and we achieve this by attempting to build as much of each of these subsystems from scratch as possible. Not only does this provide the most possible experience, but we are also able to grow our mission scope and customize our requirements without the excessive budget attached with many pre-made satellite components. We plan to present on the current and planned state of the mission, what we have learned in the process of designing and building this mission, and our next plans for further space exploration at the University of Washington.

When discussing the experiences of the Asian American community, certain ethnic subgroups tend to receive more attention, while others are sidelined: people may acknowledge Japanese internment camps or the Chinese Exclusion Act, but not the increasing occurrence of post-9/11 racial profiling targeting South Asians, or the high poverty rate among Southeast Asians. We investigate the consequences of this invisibility threat, the situation in which less prototypical subgroups are ignored and rendered invisible within their superordinate group. Prototypicality is defined as the degree to which a subgroup fits the characteristics that are strongly associated with a superordinate group. A pilot study established that Southeast Asian (e.g., Vietnamese) and South Asian (e.g., Indian) ethnic subgroups are indeed perceived to be less prototypical of the Asian American category than East Asian subgroups (e.g., Chinese). The current study uses a 2 (ethnic identity: prototypical, non-prototypical) x 2 (condition: invisibility threat, control) between-subjects design to investigate the effects of invisibility threat on Asian Americans' racial group identity (i.e., sense of belonging, racial identification) and their relationship with fellow group members (i.e., group solidarity, willingness to form coalitions with other Asian Americans). Prototypical and non-prototypical Asian American students are presented with a Wikipedia article about the demographics of the Asian American community, socioeconomic issues faced by the community, and a few notable Asian Americans. This article is either inclusive of all Asian American ethnic subgroups (control condition), or does not mention students' own ethnic subgroup (invisibility threat condition). We predict that experiencing invisibility threat will decrease non-prototypical Asian American's racial group identity and have a negative effect on their relationship with fellow group members. We hypothesize that prototypical Asian Americans will not be affected. This research has implications for the need to disaggregate Asian American data to reduce invisibility threat among Asian Americans.

Abundance estimates are integral to wildlife management. In many cases however, abundance estimates are difficult to obtain due to excessive labor and costs. Alternatively, abundance indices can provide representative measurements of relative abundance. Furthermore, cameras are a convenient tool to obtain estimates of relative abundance using capture frequencies as indices, though are predominantly used on larger animals. Small mammal abundance is commonly used to measure for forest health, diversity, and prey availability, though is generally dependent on the use of live trapping. Broadening the application of camera traps can prove to develop better indices for abundance analyses. Through this study, we examine different indices of small mammal abundance to determine whether camera trap data can be used as an index of small mammal abundance. Using data collected from the field, an abundance estimate based on live trapping of mice, voles, and chipmunks is compared to our camera trap estimates of these three species. We tested three possible small mammal indices, two of which were camera based: proportion of cameras detecting a species, number independent detection events, and number of animals live captured on the first night. Each of the three indices that were tested gave an estimate of abundance which we compared with the live-capture density estimate to determine relative accuracy. The proportion detected estimate and the first night capture estimate were significantly correlated to the estimated population abundance of each species. The low population of voles influenced the results and are discussed further. This data may contribute meaningful data for future wildlife abundance analyses. By gaining an understanding of reliable indices, we are able to make better considerations for wildlife management decisions.

Amazonian soils are notoriously nutrient-poor, making it difficult to grow crops without the use of slash and burn practices or synthetic fertilizers. Communities outside of urban areas do not have access to sufficient nutritional variation in their diets. This results in dietary deficiencies, especially in children, as well as more time and money spent importing food items from nearby cities. The objective of my research was to evaluate an approach for developing a community-centered permaculture planting plan. From January through March 2018, I interned for Hoja Nueva, which works with remote native and migrant communities that are generally neglected by the government due to their inaccessibility. The case study focused on a community located on the Las Piedras River in the Peruvian Amazon called Puerto Nuevo, which is known as the ‘forgotten village’ because it lacks an active health post, water treatment, and waste management system. In February, I conducted individual interviews about current diet and desired fruits and vegetables with villagers and held community meetings about potential garden sites. Additionally, two potential sites identified by the community were tested for macronutrient concentrations (nitrogen, phosphorus, and potassium), pH, texture, moisture levels, and environmental variables like light exposure, temperature, relative humidity, and other microclimate variables. These data were critical for determining which site will best support certain plants requested by the community. The complete permaculture plan was delivered in March and included designs for a fruiting forest and vegetable garden with native plants and a compost system to help replenish the soils. Once completed, the mature permaculture site will greatly enhance the diet of the Puerto Nuevo community. The opportunities and challenges inherent in this community-centered approach are discussed.

The California Current region encompasses a gradient between coastal upwelling and oligotrophic offshore zones, where the phytoplankton biomass is dominated by species of large and small celled phytoplankton, respectively. Mesoscale eddies are ubiquitous in the mixed region between the coastal and offshore zones, and they mediate the offshore transport of coastal waters. Mesoscale eddies are known to trap and transport water masses and their associated biogeochemical signatures, acting much like traveling mesocosms. It is unclear to what extent phytoplankton communities are trapped by the eddies, and how much they mingle with the communities found in the surrounding waters. In this study we characterized the phytoplankton community structure found within three mesoscale eddies, two cyclones and one anticyclone, using flow cytometry and 16S and 18S tag sequencing. We tracked the age and region of formation of the eddies from sea surface height. The two cyclonic eddies were formed in the same region, but at different times, C1 was 22 days old and C2 was 214 days old at the time of sampling. The anticyclonic eddy, A1, was formed further to the south and was 19 days old at the time of sampling. We assess to what extent the phytoplankton communities within each of the eddies are distinct from their surrounding waters, differ from each other, and how much the phytoplankton communities vary within each of the eddies with distance and depth. Our results show that the phytoplankton community is structured, to first order, by the physical environment, such that the phytoplankton metacommunities differ between eddies. However, we also see finer scale features with community changes within and across the eddies. These deviations reveal patchiness in the communities likely driven by corresponding local patchiness in nutrient and trace metal concentrations.

Calcific aortic valve disease (CAVD) is a disease that results in aortic valve thickening and calcification, leading to valve stenosis. It is commonly experienced by aging people, especially those suffering from type II diabetes mellitus (T2DM). There is currently no effective drug therapy to prevent or treat CAVD, mainly due to the poor understanding of its etiology. The proposed study will explore the cellular and molecular mechanisms of diabetic CAVD, focusing on transcription factors Sox9 and Runx2. As the disease progresses, Sox9-expressing cells differentiate into procalcific Runx2-expressing cells, resulting in valve calcification and stenosis. We hypothesize that Sox9-expressing cells in T2DM aortic valves are reparative. To test this hypothesis, I will feed a diabetogenic high-fat diet to a mouse model susceptible to developing CAVD, which will enable genetic fate mapping of Sox9-expressing cells upon administration of tamoxifen intraperitoneally. Aortic valve sections will then be stained with X-gal, a substrate used for detection of the transgene used for the genetic fate mapping of Sox9 cells. X-gal staining will identify cells that once expressed Sox9 and immunofluorescent staining will identify Runx2 expression in cells. Quantification of Runx2+ cells with or without X-gal+ Sox9 will determine if Runx2+ cells are derived from Sox9-expressing cells and, if so, to what extent. If Sox9+ cells indeed give rise to Runx2+ cells, colocalization in staining by X-gal and Runx2 antibody is expected. This research will help identify cellular and molecular targets that may be used as a basis for future diabetic CAVD drug therapies.

The nonnegative inverse eigenvalue problem (NIEP) is to characterize the spectra (i.e., list of eigenvalues) of entrywise nonnegative matrices. More specifically, given a finite list S = {s_1, ..., s_n} of complex numbers, the NIEP asks for necessary and sufficient conditions such that S is the spectrum of an n-by-n entrywise-nonnegative matrix. In further pursuit of a solution to the NIEP, Loewy and London posed the problem of characterizing all polynomials that preserve all nonnegative matrices of a fixed order. If P_n denote the set of all polynomials that preserve all n-by-n nonnegative matrices, then it is clear that all polynomials with nonnegative coefficients belong to P_n. However, it is known that P_n contains polynomials with negative entries. In this work we present results for P_n for all orders; we characterize all polynomial functions that preserve the nonnegativity of certain structured matrices, including circulant matrices and Jordan blocks. This work is important because once P_n is characterized, it could lead to some necessary and sufficient conditions for the NIEP. This work could also have implications in the field of matrix analysis in terms of how polynomials affect square matrices.

Natural products are often studied as treatments for chronic inflammation. In this study, the activity of the nuclear factor NF-κB pathway, a pro-inflammatory pathway, was analyzed after treatment with three different combination therapies between natural products Artesunate, Cantharidin, Parthenolide, and Withaferin A, which have all been separately shown to inhibit the NF- κB pathway. The combination therapies chosen to test were determined by Systems Biology, a bioinformatics system that uses a collaborative and integrative design from many scientific disciplines to predict how the cells’ biological system change over time and under varying conditions. The combination therapies of interest were: Artesunate and Cantharidin, Parthenolide and Withaferin A, and Cantharidin and Withaferin A. Exposure of Huh7, a human liver cell line, to the combination therapies of interest and TNF-α induced NF-κB activation. Western blot and luciferase reaction were then used to measure how different combination therapies changed NF-κB activation. The three combinations demonstrated different effects of NF-κB. Our findings will have important implications in understanding the human immune responses to diseases and how known treatments could be develop to be more effective.

Brain-Computer Interface (BCI) research is a rapidly growing area of development in biomedicine. As this neurotechnology continues to be developed it is important to address the following question: what is the most appropriate way to conceptualize BCIs from the ethical point of view? This is important to consider because how we understand the device will shape how it is developed and used in ethical discussions. Potential end-users and ethicists while beginning to investigate BCIs have identified nuanced issues specific to BCIs in the areas of privacy, security, identity and intimacy. To understand these issues physicians, scientists, ethicists and patients are conceptualizing BCIs through analogies drawn from both the medical and consumer realm. This has been shown through a comprehensive lit review and analysis of coded focus group discussions with a spinal cord injury group, a non-disabled group and a mixed group. Analogies to medical and consumer technologies, such as the cardiac pacemaker, wheelchair and iPhone, were most commonly drawn from. Although descriptive, these analogies do not fully encompass the nuanced issues presented by BCIs. Drawing on analogies that do capture these nuances could change the direction of our research, miscommunicate risks to patients or change the way we fundamentally understand brains and computers.

Gender disparities in healthcare are still prevalent in many societies today. Previous research has shown that women with heart disease are more likely to get misdiagnosed or diagnosed later than men. In fact, young women with heart disease have a mortality twice as high as young men. Because many medical conditions, heart disease included, present differing symptoms between men and women, (and so) they require gender-sensitive diagnostic and therapeutic strategies. In a case study at the UW, I will be observing and interviewing women’s healthcare internal medicine specialists. I aim to learn from participants what brought them to this specialty, what trajectories bring patients to these clinicians rather than general internal medicine specialists. I am also recording any gender-specific diagnostic and therapeutic approaches the clinicians used as well as giving an overview of the medical residents’ training in the women’s healthcare track. Hopefully, this data could help illustrate current strengths and limitations of having a women’s healthcare track within medical specialties, and the implications this track might have for reducing gender health disparities.

Social-economic disparity has been shown to be one of the most significant risk factors influencing population health. Some factors that project this disparity include accessibility to fresh food options, green spaces, and healthcare; these amenities are unevenly distributed geographically similar to disease occurrence patterns. In this study, we use a geographic information system (GIS) framework to depict the relationship between cardiovascular disease induced mortality rate and accessibility to services such as farmer's markets, food facilities, parks, and health insurance in King County at the census tract level (N=397). We also used the target population's demographic information such as age distribution, sex ratio, ethnicity, and population density in each census tract as our control variables. We used spatial regression to test the relationships between independent and dependent variables. Our results indicate that the number of people with insurance, Asian and White ethnicity appear to be statistically correlated at a 0.05 significance level. The results of this study show the possibility of predicting risk factors of population's cardiovascular health through the integration of public health and spatial analysis.